proteore_data_manager: data_manager/resource

annotate data_manager/resource_building.py @ 48:09d9fd9b2d8c draft

"planemo upload commit 714703437f238e7295980f96620365b801fd435c-dirty"

author	proteore
date	Fri, 31 Jan 2020 15:51:40 +0000
parents	488e015576bc
children	1c40456be1db

rev	line source
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	1 # -- coding: utf-8 --
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	2 """
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	3 The purpose of this script is to create source files from different databases to be used in other proteore tools
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	4 """
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	5
42 f6a6a70712c4 "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 41 diff changeset	6 import os, shutil, sys, argparse, requests, time, csv, re, json, shutil, zipfile, subprocess
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	7 from io import BytesIO
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	8 from zipfile import ZipFile
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	9 from galaxy.util.json import from_json_string, to_json_string
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	10
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	11 #######################################################################################################
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	12 # General functions
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	13 #######################################################################################################
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	14 def unzip(url, output_file):
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	15 """
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	16 Get a zip file content from a link and unzip
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	17 """
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	18 content = requests.get(url)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	19 zipfile = ZipFile(BytesIO(content.content))
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	20 output_content = ""
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	21 output_content += zipfile.open(zipfile.namelist()[0]).read()
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	22 output = open(output_file, "w")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	23 output.write(output_content)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	24 output.close()
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	25
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	26 def _add_data_table_entry(data_manager_dict, data_table_entry,data_table):
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	27 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	28 data_manager_dict['data_tables'][data_table] = data_manager_dict['data_tables'].get(data_table, [])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	29 data_manager_dict['data_tables'][data_table].append(data_table_entry)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	30 return data_manager_dict
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	31
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	32 #######################################################################################################
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	33 # 1. Human Protein Atlas
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	34 # - Normal tissue
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	35 # - Pathology
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	36 # - Full Atlas
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	37 #######################################################################################################
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	38 def HPA_sources(data_manager_dict, tissue, target_directory):
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	39 if tissue == "HPA_normal_tissue":
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	40 tissue_name = "HPA normal tissue"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	41 url = "https://www.proteinatlas.org/download/normal_tissue.tsv.zip"
1 0915249b8c4b planemo upload commit 4dd1a2f7d196a1d2e70fab379a2c08367da0fe94-dirty proteore parents: 0 diff changeset	42 table = "proteore_protein_atlas_normal_tissue"
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	43 elif tissue == "HPA_pathology":
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	44 tissue_name = "HPA pathology"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	45 url = "https://www.proteinatlas.org/download/pathology.tsv.zip"
1 0915249b8c4b planemo upload commit 4dd1a2f7d196a1d2e70fab379a2c08367da0fe94-dirty proteore parents: 0 diff changeset	46 table = "proteore_protein_atlas_tumor_tissue"
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	47 elif tissue == "HPA_full_atlas":
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	48 tissue_name = "HPA full atlas"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	49 url = "https://www.proteinatlas.org/download/proteinatlas.tsv.zip"
1 0915249b8c4b planemo upload commit 4dd1a2f7d196a1d2e70fab379a2c08367da0fe94-dirty proteore parents: 0 diff changeset	50 table = "proteore_protein_full_atlas"
48 09d9fd9b2d8c "planemo upload commit 714703437f238e7295980f96620365b801fd435c-dirty" proteore parents: 45 diff changeset	51 elif tissue == "HPA_RNA_tissue":
09d9fd9b2d8c "planemo upload commit 714703437f238e7295980f96620365b801fd435c-dirty" proteore parents: 45 diff changeset	52 tissue_name = "HPA RNA tissue"
09d9fd9b2d8c "planemo upload commit 714703437f238e7295980f96620365b801fd435c-dirty" proteore parents: 45 diff changeset	53 url = "https://www.proteinatlas.org/download/normal_tissue.tsv.zip"
09d9fd9b2d8c "planemo upload commit 714703437f238e7295980f96620365b801fd435c-dirty" proteore parents: 45 diff changeset	54 table = "proteore_protein_atlas_rna_tissue"
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	55
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	56 output_file = tissue +"_"+ time.strftime("%d-%m-%Y") + ".tsv"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	57 path = os.path.join(target_directory, output_file)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	58 unzip(url, path) #download and save file
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	59 tissue_name = tissue_name + " " + time.strftime("%d/%m/%Y")
26 bf6940ff60a8 planemo upload commit 0290724216a2c445b4e28842153b84a1b28f4e9a-dirty proteore parents: 24 diff changeset	60 release = tissue_name.replace(" ","_").replace("/","-")
bf6940ff60a8 planemo upload commit 0290724216a2c445b4e28842153b84a1b28f4e9a-dirty proteore parents: 24 diff changeset	61 id = str(10000000000 - int(time.strftime("%Y%m%d")))
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	62
1 0915249b8c4b planemo upload commit 4dd1a2f7d196a1d2e70fab379a2c08367da0fe94-dirty proteore parents: 0 diff changeset	63
26 bf6940ff60a8 planemo upload commit 0290724216a2c445b4e28842153b84a1b28f4e9a-dirty proteore parents: 24 diff changeset	64 data_table_entry = dict(id=id, release=release, name = tissue_name, tissue = tissue, value = path)
1 0915249b8c4b planemo upload commit 4dd1a2f7d196a1d2e70fab379a2c08367da0fe94-dirty proteore parents: 0 diff changeset	65 _add_data_table_entry(data_manager_dict, data_table_entry, table)
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	66
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	67
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	68 #######################################################################################################
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	69 # 2. Peptide Atlas
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	70 #######################################################################################################
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	71 def peptide_atlas_sources(data_manager_dict, tissue, date, target_directory):
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	72 # Define organism_id (here Human) - to be upraded when other organism added to the project
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	73 organism_id = "2"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	74 # Extract sample_category_id and output filename
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	75 tissue=tissue.split(".")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	76 sample_category_id = tissue[0]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	77 tissue_name = tissue[1]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	78 output_file = tissue_name+"_"+date + ".tsv"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	79
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	80 query="https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProteins?&atlas_build_id="+ \
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	81 sample_category_id+"&display_options=ShowAbundances&organism_id="+organism_id+ \
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	82 "&redundancy_constraint=4&presence_level_constraint=1%2C2&gene_annotation_level_constraint=leaf\
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	83 &QUERY_NAME=AT_GetProteins&action=QUERY&output_mode=tsv&apply_action=QUERY"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	84
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	85 with requests.Session() as s:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	86 download = s.get(query)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	87 decoded_content = download.content.decode('utf-8')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	88 cr = csv.reader(decoded_content.splitlines(), delimiter='\t')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	89
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	90 uni_dict = build_dictionary(cr)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	91
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	92 #columns of data table peptide_atlas
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	93 tissue_id = tissue_name+"_"+date
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	94 name = tissue_id.replace("-","/").replace("_"," ")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	95 path = os.path.join(target_directory,output_file)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	96
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	97 with open(path,"w") as out :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	98 w = csv.writer(out,delimiter='\t')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	99 w.writerow(["Uniprot_AC","nb_obs"])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	100 w.writerows(uni_dict.items())
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	101
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	102 data_table_entry = dict(id=tissue_id, name=name, value = path, tissue = tissue_name)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	103 _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_peptide_atlas")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	104
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	105 #function to count the number of observations by uniprot id
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	106 def build_dictionary (csv) :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	107 uni_dict = {}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	108 for line in csv :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	109 if "-" not in line[0] and check_uniprot_access(line[0]) :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	110 if line[0] in uni_dict :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	111 uni_dict[line[0]] += int(line[5])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	112 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	113 uni_dict[line[0]] = int(line[5])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	114
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	115 return uni_dict
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	116
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	117 #function to check if an id is an uniprot accession number : return True or False-
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	118 def check_uniprot_access (id) :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	119 uniprot_pattern = re.compile("[OPQ][0-9][A-Z0-9]{3}[0-9]\|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2}")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	120 if uniprot_pattern.match(id) :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	121 return True
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	122 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	123 return False
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	124
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	125 def check_entrez_geneid (id) :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	126 entrez_pattern = re.compile("[0-9]+\|[A-Z]{1,2}_[0-9]+\|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	127 if entrez_pattern.match(id) :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	128 return True
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	129 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	130 return False
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	131
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	132 #######################################################################################################
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	133 # 3. ID mapping file
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	134 #######################################################################################################
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	135 import ftplib, gzip
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	136 csv.field_size_limit(sys.maxsize) # to handle big files
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	137
31 faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	138 def id_mapping_sources (data_manager_dict, species, target_directory, tool_data_path) :
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	139
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	140 human = species == "Human"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	141 species_dict = { "Human" : "HUMAN_9606", "Mouse" : "MOUSE_10090", "Rat" : "RAT_10116" }
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	142 files=["idmapping_selected.tab.gz","idmapping.dat.gz"]
36 b18cb0d11971 "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 35 diff changeset	143 archive = os.path.join(tool_data_path, "id_mapping/ID_mapping_archive_"+species+"_"+str(time.strftime("%Y%m%d")))
38 6daab0a711e2 "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 37 diff changeset	144 if os.path.isdir(archive) is False : os.mkdir(archive)
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	145
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	146 #header
30 a6cabd3ab71f "planemo upload commit b89f1921a1759139b452c6fac1ad7ee01b6b633d-dirty" proteore parents: 29 diff changeset	147 if human : tab = [["UniProt-AC","UniProt-AC_reviewed","UniProt-ID","GeneID","RefSeq","GI","PDB","GO","PIR","MIM","UniGene","Ensembl_Gene","Ensembl_Transcript","Ensembl_Protein","neXtProt","BioGrid","STRING","KEGG",'Gene_Name']]
a6cabd3ab71f "planemo upload commit b89f1921a1759139b452c6fac1ad7ee01b6b633d-dirty" proteore parents: 29 diff changeset	148 else : tab = [["UniProt-AC","UniProt-AC_reviewed","UniProt-ID","GeneID","RefSeq","GI","PDB","GO","PIR","MIM","UniGene","Ensembl_Gene","Ensembl_Transcript","Ensembl_Protein","BioGrid","STRING","KEGG",'Gene_Name']]
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	149
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	150 #get selected.tab and keep only ids of interest
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	151 selected_tab_file=species_dict[species]+"_"+files[0]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	152 tab_path = download_from_uniprot_ftp(selected_tab_file,target_directory)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	153 with gzip.open(tab_path,"rt") as select :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	154 tab_reader = csv.reader(select,delimiter="\t")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	155 for line in tab_reader :
30 a6cabd3ab71f "planemo upload commit b89f1921a1759139b452c6fac1ad7ee01b6b633d-dirty" proteore parents: 29 diff changeset	156 tab.append([line[0]]+[line[i] for i in [0,1,2,3,4,5,6,11,13,14,18,19,20]])
41 fe21769281fa "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 40 diff changeset	157 if os.path.exists(os.path.join(archive,tab_path.split("/")[-1])) : os.remove(os.path.join(archive,tab_path.split("/")[-1]))
31 faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	158 shutil.move(tab_path, archive)
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	159 #print("selected_tab ok")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	160
20 29cf75c83618 planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 16 diff changeset	161 #get uniprot-AC reviewed
22 4296fb613d9d planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 21 diff changeset	162 organism = species_dict[species].split("_")[1]
4296fb613d9d planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 21 diff changeset	163 query = "https://www.uniprot.org/uniprot/?query=reviewed:yes+AND+organism:"+organism+"&format=list"
20 29cf75c83618 planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 16 diff changeset	164
29cf75c83618 planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 16 diff changeset	165 with requests.Session() as s:
29cf75c83618 planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 16 diff changeset	166 download = s.get(query)
29cf75c83618 planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 16 diff changeset	167 decoded_content = download.content.decode('utf-8')
29cf75c83618 planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 16 diff changeset	168 uniprot_reviewed_list = decoded_content.splitlines()
29cf75c83618 planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 16 diff changeset	169
31 faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	170 #save reviewed list
faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	171 reviewed_list_path = os.path.join(archive,'uniprot_reviewed_list.txt')
34 06b3181206b4 "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 33 diff changeset	172 with open(reviewed_list_path,'w') as reviewed_list_file:
31 faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	173 for id in uniprot_reviewed_list:
faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	174 reviewed_list_file.write(id+"\n")
faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	175
faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	176 #remove unreviewed uniprot-AC
20 29cf75c83618 planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 16 diff changeset	177 for line in tab[1:]:
30 a6cabd3ab71f "planemo upload commit b89f1921a1759139b452c6fac1ad7ee01b6b633d-dirty" proteore parents: 29 diff changeset	178 UniProtAC = line[1]
28 808c8493ed4f planemo upload commit 5c2c274361c0daceae1f678eca0e6c0d5b4ba4f7-dirty proteore parents: 27 diff changeset	179 if UniProtAC not in uniprot_reviewed_list :
29 9a40b72414de planemo upload commit 3c02acc07df862410ce979ce63e3d14f10edc50f-dirty proteore parents: 28 diff changeset	180 line[1]=""
20 29cf75c83618 planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 16 diff changeset	181
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	182 """
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	183 Supplementary ID to get from HUMAN_9606_idmapping.dat :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	184 -NextProt,BioGrid,STRING,KEGG
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	185 """
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	186
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	187 #there's more id type for human
30 a6cabd3ab71f "planemo upload commit b89f1921a1759139b452c6fac1ad7ee01b6b633d-dirty" proteore parents: 29 diff changeset	188 if human : ids = ['neXtProt','BioGrid','STRING','KEGG','Gene_Name' ] #ids to get from dat_file
a6cabd3ab71f "planemo upload commit b89f1921a1759139b452c6fac1ad7ee01b6b633d-dirty" proteore parents: 29 diff changeset	189 else : ids = ['BioGrid','STRING','KEGG','Gene_Name' ]
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	190 unidict = {}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	191
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	192 #keep only ids of interest in dictionaries
40 a7bcc9a0a456 "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 39 diff changeset	193 dat_file = species_dict[species]+"_"+files[1]
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	194 dat_path = download_from_uniprot_ftp(dat_file,target_directory)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	195 with gzip.open(dat_path,"rt") as dat :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	196 dat_reader = csv.reader(dat,delimiter="\t")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	197 for line in dat_reader :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	198 uniprotID=line[0] #UniProtID as key
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	199 id_type=line[1] #ID type of corresponding id, key of sub-dictionnary
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	200 cor_id=line[2] #corresponding id
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	201 if "-" not in id_type : #we don't keep isoform
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	202 if id_type in ids and uniprotID in unidict :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	203 if id_type in unidict[uniprotID] :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	204 unidict[uniprotID][id_type]= ";".join([unidict[uniprotID][id_type],cor_id]) #if there is already a value in the dictionnary
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	205 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	206 unidict[uniprotID].update({ id_type : cor_id })
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	207 elif id_type in ids :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	208 unidict[uniprotID]={id_type : cor_id}
41 fe21769281fa "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 40 diff changeset	209 if os.path.exists(os.path.join(archive,dat_path.split("/")[-1])) : os.remove(os.path.join(archive,dat_path.split("/")[-1]))
31 faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	210 shutil.move(dat_path, archive)
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	211
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	212 #print("dat_file ok")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	213
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	214 #add ids from idmapping.dat to the final tab
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	215 for line in tab[1:] :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	216 uniprotID=line[0]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	217 if human :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	218 if uniprotID in unidict :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	219 nextprot = access_dictionary(unidict,uniprotID,'neXtProt')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	220 if nextprot != '' : nextprot = clean_nextprot_id(nextprot,line[0])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	221 line.extend([nextprot,access_dictionary(unidict,uniprotID,'BioGrid'),access_dictionary(unidict,uniprotID,'STRING'),
30 a6cabd3ab71f "planemo upload commit b89f1921a1759139b452c6fac1ad7ee01b6b633d-dirty" proteore parents: 29 diff changeset	222 access_dictionary(unidict,uniprotID,'KEGG'),access_dictionary(unidict,uniprotID,'Gene_Name')])
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	223 else :
30 a6cabd3ab71f "planemo upload commit b89f1921a1759139b452c6fac1ad7ee01b6b633d-dirty" proteore parents: 29 diff changeset	224 line.extend(["","","","",""])
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	225 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	226 if uniprotID in unidict :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	227 line.extend([access_dictionary(unidict,uniprotID,'BioGrid'),access_dictionary(unidict,uniprotID,'STRING'),
30 a6cabd3ab71f "planemo upload commit b89f1921a1759139b452c6fac1ad7ee01b6b633d-dirty" proteore parents: 29 diff changeset	228 access_dictionary(unidict,uniprotID,'KEGG'),access_dictionary(unidict,uniprotID,'Gene_Name')])
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	229 else :
30 a6cabd3ab71f "planemo upload commit b89f1921a1759139b452c6fac1ad7ee01b6b633d-dirty" proteore parents: 29 diff changeset	230 line.extend(["","","",""])
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	231
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	232 #print ("tab ok")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	233
20 29cf75c83618 planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 16 diff changeset	234 #add missing nextprot ID for human or replace old ones
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	235 if human :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	236 #build next_dict
31 faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	237 nextprot_path = id_list_from_nextprot_ftp("nextprot_ac_list_all.txt",target_directory)
faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	238 with open(nextprot_path,'r') as nextprot_ids :
faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	239 nextprot_ids = nextprot_ids.read().splitlines()
41 fe21769281fa "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 40 diff changeset	240 if os.path.exists(os.path.join(archive,nextprot_path.split("/")[-1])) : os.remove(os.path.join(archive,nextprot_path.split("/")[-1]))
31 faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	241 shutil.move(nextprot_path,archive)
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	242 next_dict = {}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	243 for nextid in nextprot_ids :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	244 next_dict[nextid.replace("NX_","")] = nextid
45 488e015576bc "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 44 diff changeset	245 #os.remove(os.path.join(target_directory,"nextprot_ac_list_all.txt"))
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	246
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	247 #add missing nextprot ID
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	248 for line in tab[1:] :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	249 uniprotID=line[0]
30 a6cabd3ab71f "planemo upload commit b89f1921a1759139b452c6fac1ad7ee01b6b633d-dirty" proteore parents: 29 diff changeset	250 nextprotID=line[14]
20 29cf75c83618 planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 16 diff changeset	251 if uniprotID in next_dict and (nextprotID == '' or (nextprotID != "NX_"+uniprotID and next_dict[uniprotID] == "NX_"+uniprotID)) :
30 a6cabd3ab71f "planemo upload commit b89f1921a1759139b452c6fac1ad7ee01b6b633d-dirty" proteore parents: 29 diff changeset	252 line[14]=next_dict[uniprotID]
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	253
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	254 output_file = species+"_id_mapping_"+ time.strftime("%d-%m-%Y") + ".tsv"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	255 path = os.path.join(target_directory,output_file)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	256
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	257 with open(path,"w") as out :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	258 w = csv.writer(out,delimiter='\t')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	259 w.writerows(tab)
31 faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	260
36 b18cb0d11971 "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 35 diff changeset	261 subprocess.call(['tar', '-czvf', archive+".tar.gz", archive])
44 7ebbf851598e "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 43 diff changeset	262 shutil.rmtree(archive, ignore_errors=True)
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	263
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	264 name_dict={"Human" : "Homo sapiens", "Mouse" : "Mus musculus", "Rat" : "Rattus norvegicus"}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	265 name = species +" (" + name_dict[species]+" "+time.strftime("%d/%m/%Y")+")"
21 026177e4ff4b planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 20 diff changeset	266 release = species+"_id_mapping_"+ time.strftime("%d-%m-%Y")
23 ebdd4961c6c2 planemo upload commit 03015f58ac7e7ba3cc44ba0d8899eacfaaf5a134-dirty proteore parents: 22 diff changeset	267 id = str(10000000000 - int(time.strftime("%Y%m%d"))) #new ids must be inferior to previous id -> sort by <filter> in xml only in descending order
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	268
21 026177e4ff4b planemo upload commit e05ccbf13c33b97ab441e2f8bc4b5bc746a378df-dirty proteore parents: 20 diff changeset	269 data_table_entry = dict(id=id, release=release , name = name, species = species, value = path)
2 2e34ee6d2d37 planemo upload commit 4dd1a2f7d196a1d2e70fab379a2c08367da0fe94-dirty proteore parents: 1 diff changeset	270 _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_id_mapping_"+species)
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	271
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	272 def download_from_uniprot_ftp(file,target_directory) :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	273 ftp_dir = "pub/databases/uniprot/current_release/knowledgebase/idmapping/by_organism/"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	274 path = os.path.join(target_directory, file)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	275 ftp = ftplib.FTP("ftp.uniprot.org")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	276 ftp.login("anonymous", "anonymous")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	277 ftp.cwd(ftp_dir)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	278 ftp.retrbinary("RETR " + file, open(path, 'wb').write)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	279 ftp.quit()
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	280 return (path)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	281
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	282 def id_list_from_nextprot_ftp(file,target_directory) :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	283 ftp_dir = "pub/current_release/ac_lists/"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	284 path = os.path.join(target_directory, file)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	285 ftp = ftplib.FTP("ftp.nextprot.org")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	286 ftp.login("anonymous", "anonymous")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	287 ftp.cwd(ftp_dir)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	288 ftp.retrbinary("RETR " + file, open(path, 'wb').write)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	289 ftp.quit()
31 faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	290
faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	291 return (path)
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	292
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	293 #return '' if there's no value in a dictionary, avoid error
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	294 def access_dictionary (dico,key1,key2) :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	295 if key1 in dico :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	296 if key2 in dico[key1] :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	297 return (dico[key1][key2])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	298 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	299 return ("")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	300 #print (key2,"not in ",dico,"[",key1,"]")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	301 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	302 return ('')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	303
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	304 #if there are several nextprot ID for one uniprotID, return the uniprot like ID
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	305 def clean_nextprot_id (next_id,uniprotAc) :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	306 if len(next_id.split(";")) > 1 :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	307 tmp = next_id.split(";")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	308 if "NX_"+uniprotAc in tmp :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	309 return ("NX_"+uniprotAc)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	310 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	311 return (tmp[1])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	312 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	313 return (next_id)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	314
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	315
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	316 #######################################################################################################
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	317 # 4. Build protein interaction maps files
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	318 #######################################################################################################
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	319
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	320 def get_interactant_name(line,dico):
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	321
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	322 if line[0] in dico :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	323 interactant_A = dico[line[0]]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	324 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	325 interactant_A = "NA"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	326
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	327 if line[1] in dico :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	328 interactant_B = dico[line[1]]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	329 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	330 interactant_B = "NA"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	331
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	332 return interactant_A, interactant_B
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	333
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	334 def PPI_ref_files(data_manager_dict, species, interactome, target_directory):
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	335
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	336 species_dict={'Human':'Homo sapiens',"Mouse":"Mus musculus","Rat":"Rattus norvegicus"}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	337
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	338 ##BioGRID
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	339 if interactome=="biogrid":
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	340
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	341 tab2_link="https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-3.5.167/BIOGRID-ORGANISM-3.5.167.tab2.zip"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	342
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	343 #download zip file
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	344 r = requests.get(tab2_link)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	345 with open("BioGRID.zip", "wb") as code:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	346 code.write(r.content)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	347
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	348 #unzip files
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	349 with zipfile.ZipFile("BioGRID.zip", 'r') as zip_ref:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	350 if not os.path.exists("tmp_BioGRID"): os.makedirs("tmp_BioGRID")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	351 zip_ref.extractall("tmp_BioGRID")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	352
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	353 #import file of interest and build dictionary
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	354 file_path="tmp_BioGRID/BIOGRID-ORGANISM-"+species_dict[species].replace(" ","_")+"-3.5.167.tab2.txt"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	355 with open(file_path,"r") as handle :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	356 tab_file = csv.reader(handle,delimiter="\t")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	357 dico_network = {}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	358 GeneID_index=1
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	359 network_cols=[1,2,7,8,11,12,14,18,20]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	360 for line in tab_file :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	361 if line[GeneID_index] not in dico_network:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	362 dico_network[line[GeneID_index]]=[[line[i] for i in network_cols]]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	363 else:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	364 dico_network[line[GeneID_index]].append([line[i] for i in network_cols])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	365
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	366 #delete tmp_BioGRID directory
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	367 os.remove("BioGRID.zip")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	368 shutil.rmtree("tmp_BioGRID", ignore_errors=True)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	369
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	370 #download NCBI2Reactome.txt file and build dictionary
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	371 with requests.Session() as s:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	372 r = s.get('https://www.reactome.org/download/current/NCBI2Reactome.txt')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	373 r.encoding ="utf-8"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	374 tab_file = csv.reader(r.content.splitlines(), delimiter='\t')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	375
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	376 dico_nodes = {}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	377 geneid_index=0
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	378 pathway_description_index=3
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	379 species_index=5
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	380 for line in tab_file :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	381 if line[species_index]==species_dict[species]:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	382 if line[geneid_index] in dico_nodes :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	383 dico_nodes[line[geneid_index]].append(line[pathway_description_index])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	384 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	385 dico_nodes[line[geneid_index]] = [line[pathway_description_index]]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	386
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	387 dico={}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	388 dico['network']=dico_network
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	389 dico['nodes']=dico_nodes
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	390
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	391 ##Bioplex
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	392 elif interactome=="bioplex":
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	393
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	394 with requests.Session() as s:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	395 r = s.get('http://bioplex.hms.harvard.edu/data/BioPlex_interactionList_v4a.tsv')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	396 r = r.content.decode('utf-8')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	397 bioplex = csv.reader(r.splitlines(), delimiter='\t')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	398
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	399 dico_network = {}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	400 dico_network["GeneID"]={}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	401 network_geneid_cols=[0,1,4,5,8]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	402 dico_network["UniProt-AC"]={}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	403 network_uniprot_cols=[2,3,4,5,8]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	404 dico_GeneID_to_UniProt = {}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	405 for line in bioplex :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	406 if line[0] not in dico_network["GeneID"]:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	407 dico_network["GeneID"][line[0]]=[[line[i] for i in network_geneid_cols]]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	408 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	409 dico_network["GeneID"][line[0]].append([line[i] for i in network_geneid_cols])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	410 if line[1] not in dico_network["UniProt-AC"]:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	411 dico_network["UniProt-AC"][line[2]]=[[line[i] for i in network_uniprot_cols]]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	412 else:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	413 dico_network["UniProt-AC"][line[2]].append([line[i] for i in network_uniprot_cols])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	414 dico_GeneID_to_UniProt[line[0]]=line[2]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	415
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	416 with requests.Session() as s:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	417 r = s.get('https://reactome.org/download/current/UniProt2Reactome.txt')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	418 r.encoding ="utf-8"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	419 tab_file = csv.reader(r.content.splitlines(), delimiter='\t')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	420
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	421 dico_nodes_uniprot = {}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	422 uniProt_index=0
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	423 pathway_description_index=3
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	424 species_index=5
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	425 for line in tab_file :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	426 if line[species_index]==species_dict[species]:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	427 if line[uniProt_index] in dico_nodes_uniprot :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	428 dico_nodes_uniprot[line[uniProt_index]].append(line[pathway_description_index])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	429 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	430 dico_nodes_uniprot[line[uniProt_index]] = [line[pathway_description_index]]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	431
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	432 with requests.Session() as s:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	433 r = s.get('https://www.reactome.org/download/current/NCBI2Reactome.txt')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	434 r.encoding ="utf-8"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	435 tab_file = csv.reader(r.content.splitlines(), delimiter='\t')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	436
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	437 dico_nodes_geneid = {}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	438 geneid_index=0
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	439 pathway_description_index=3
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	440 species_index=5
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	441 for line in tab_file :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	442 if line[species_index]==species_dict[species]:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	443 if line[geneid_index] in dico_nodes_geneid :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	444 dico_nodes_geneid[line[geneid_index]].append(line[pathway_description_index])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	445 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	446 dico_nodes_geneid[line[geneid_index]] = [line[pathway_description_index]]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	447
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	448 dico={}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	449 dico_nodes={}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	450 dico_nodes['GeneID']=dico_nodes_geneid
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	451 dico_nodes['UniProt-AC']=dico_nodes_uniprot
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	452 dico['network']=dico_network
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	453 dico['nodes']=dico_nodes
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	454 dico['convert']=dico_GeneID_to_UniProt
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	455
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	456 ##Humap
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	457 elif interactome=="humap":
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	458
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	459 with requests.Session() as s:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	460 r = s.get('http://proteincomplexes.org/static/downloads/nodeTable.txt')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	461 r = r.content.decode('utf-8')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	462 humap_nodes = csv.reader(r.splitlines(), delimiter=',')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	463
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	464 dico_geneid_to_gene_name={}
9 cdd29444e0af planemo upload commit 71363136045353f422ff98219c1eb84f6fc6193a-dirty proteore parents: 8 diff changeset	465 dico_protein_name={}
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	466 for line in humap_nodes :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	467 if check_entrez_geneid(line[4]):
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	468 if line[4] not in dico_geneid_to_gene_name:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	469 dico_geneid_to_gene_name[line[4]]=line[3]
9 cdd29444e0af planemo upload commit 71363136045353f422ff98219c1eb84f6fc6193a-dirty proteore parents: 8 diff changeset	470 if line[4] not in dico_protein_name:
cdd29444e0af planemo upload commit 71363136045353f422ff98219c1eb84f6fc6193a-dirty proteore parents: 8 diff changeset	471 dico_protein_name[line[4]]=line[5]
cdd29444e0af planemo upload commit 71363136045353f422ff98219c1eb84f6fc6193a-dirty proteore parents: 8 diff changeset	472
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	473 with requests.Session() as s:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	474 r = s.get('http://proteincomplexes.org/static/downloads/pairsWprob.txt')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	475 r = r.content.decode('utf-8')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	476 humap = csv.reader(r.splitlines(), delimiter='\t')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	477
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	478 dico_network = {}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	479 for line in humap :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	480 if check_entrez_geneid(line[0]) and check_entrez_geneid(line[1]):
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	481
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	482 interactant_A, interactant_B = get_interactant_name(line,dico_geneid_to_gene_name)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	483
4 ce01295cd601 planemo upload commit 51fc514a85c1055cab5bb6e76c90f3da7e648101-dirty proteore parents: 3 diff changeset	484 #first interactant (first column)
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	485 if line[0] not in dico_network:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	486 dico_network[line[0]]=[line[:2]+[interactant_A,interactant_B,line[2]]]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	487 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	488 dico_network[line[0]].append(line[:2]+[interactant_A,interactant_B,line[2]])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	489
4 ce01295cd601 planemo upload commit 51fc514a85c1055cab5bb6e76c90f3da7e648101-dirty proteore parents: 3 diff changeset	490 #second interactant (second column)
ce01295cd601 planemo upload commit 51fc514a85c1055cab5bb6e76c90f3da7e648101-dirty proteore parents: 3 diff changeset	491 if line[1] not in dico_network:
5 429e7481c392 planemo upload commit 51fc514a85c1055cab5bb6e76c90f3da7e648101-dirty proteore parents: 4 diff changeset	492 dico_network[line[1]]=[[line[1],line[0],interactant_B,interactant_A,line[2]]]
4 ce01295cd601 planemo upload commit 51fc514a85c1055cab5bb6e76c90f3da7e648101-dirty proteore parents: 3 diff changeset	493 else :
5 429e7481c392 planemo upload commit 51fc514a85c1055cab5bb6e76c90f3da7e648101-dirty proteore parents: 4 diff changeset	494 dico_network[line[1]].append([line[1],line[0],interactant_B,interactant_A,line[2]])
4 ce01295cd601 planemo upload commit 51fc514a85c1055cab5bb6e76c90f3da7e648101-dirty proteore parents: 3 diff changeset	495
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	496 with requests.Session() as s:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	497 r = s.get('https://www.reactome.org/download/current/NCBI2Reactome.txt')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	498 r.encoding ="utf-8"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	499 tab_file = csv.reader(r.content.splitlines(), delimiter='\t')
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	500
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	501 dico_nodes = {}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	502 geneid_index=0
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	503 pathway_description_index=3
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	504 species_index=5
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	505 for line in tab_file :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	506 if line[species_index]==species_dict[species]:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	507 #Fill dictionary with pathways
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	508 if line[geneid_index] in dico_nodes :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	509 dico_nodes[line[geneid_index]].append(line[pathway_description_index])
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	510 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	511 dico_nodes[line[geneid_index]] = [line[pathway_description_index]]
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	512
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	513 dico={}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	514 dico['network']=dico_network
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	515 dico['nodes']=dico_nodes
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	516 dico['gene_name']=dico_geneid_to_gene_name
9 cdd29444e0af planemo upload commit 71363136045353f422ff98219c1eb84f6fc6193a-dirty proteore parents: 8 diff changeset	517 dico['protein_name']=dico_protein_name
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	518
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	519 #writing output
27 9a400ce8e4e6 planemo upload commit bb113d19d3a756f70784e6a1433902888686ed96-dirty proteore parents: 26 diff changeset	520 output_file = species+'_'+interactome+'_'+ time.strftime("%Y-%m-%d") + ".json"
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	521 path = os.path.join(target_directory,output_file)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	522 name = species+" ("+species_dict[species]+") "+time.strftime("%d/%m/%Y")
27 9a400ce8e4e6 planemo upload commit bb113d19d3a756f70784e6a1433902888686ed96-dirty proteore parents: 26 diff changeset	523 release = species+"_"+interactome+"_"+ time.strftime("%Y-%m-%d")
26 bf6940ff60a8 planemo upload commit 0290724216a2c445b4e28842153b84a1b28f4e9a-dirty proteore parents: 24 diff changeset	524 id = str(10000000000 - int(time.strftime("%Y%m%d")))
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	525
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	526 with open(path, 'w') as handle:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	527 json.dump(dico, handle, sort_keys=True)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	528
26 bf6940ff60a8 planemo upload commit 0290724216a2c445b4e28842153b84a1b28f4e9a-dirty proteore parents: 24 diff changeset	529 data_table_entry = dict(id=id, release=release, name = name, species = species, value = path)
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	530 _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_"+interactome+"_dictionaries")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	531
6 f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	532 #######################################################################################################
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	533 # 5. nextprot (add protein features)
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	534 #######################################################################################################
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	535
8 d5badf9de1b0 planemo upload commit 968cd5b4f78f0a1da86fc3bc29f8159f86e199aa-dirty proteore parents: 6 diff changeset	536 def Build_nextprot_ref_file(data_manager_dict,target_directory):
6 f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	537 nextprot_ids_file = "nextprot_ac_list_all.txt"
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	538 ids = id_list_from_nextprot_ftp(nextprot_ids_file,target_directory)
12 f6afaa1f562c planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c-dirty proteore parents: 11 diff changeset	539
f6afaa1f562c planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c-dirty proteore parents: 11 diff changeset	540 output_file = 'nextprot_ref_'+ time.strftime("%d-%m-%Y") + ".tsv"
f6afaa1f562c planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c-dirty proteore parents: 11 diff changeset	541 path = os.path.join(target_directory,output_file)
f6afaa1f562c planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c-dirty proteore parents: 11 diff changeset	542 name = "neXtProt release "+time.strftime("%d-%m-%Y")
16 f75c525e0a4a planemo upload commit 04868e380c43447fac1309fc292785d67863a87b-dirty proteore parents: 15 diff changeset	543 release_id = "nextprot_ref_"+time.strftime("%d-%m-%Y")
12 f6afaa1f562c planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c-dirty proteore parents: 11 diff changeset	544
13 098693479a9d planemo upload commit 64366857c1f29dd79a77dc331eb0153cb94cdb11 proteore parents: 12 diff changeset	545 output = open(path, 'w')
098693479a9d planemo upload commit 64366857c1f29dd79a77dc331eb0153cb94cdb11 proteore parents: 12 diff changeset	546 writer = csv.writer(output,delimiter="\t")
12 f6afaa1f562c planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c-dirty proteore parents: 11 diff changeset	547
6 f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	548 nextprot_file=[["NextprotID","MW","SeqLength","IsoPoint","Chr","SubcellLocations","Diseases","TMDomains","ProteinExistence"]]
14 3f9ba522bfe8 planemo upload commit 272d182247f4fa55a928ec8cdcb83eab50c7f6ef proteore parents: 13 diff changeset	549 writer.writerows(nextprot_file)
3f9ba522bfe8 planemo upload commit 272d182247f4fa55a928ec8cdcb83eab50c7f6ef proteore parents: 13 diff changeset	550
6 f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	551 for id in ids :
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	552 #print (id)
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	553 query="https://api.nextprot.org/entry/"+id+".json"
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	554 resp = requests.get(url=query)
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	555 data = resp.json()
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	556
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	557 #get info from json dictionary
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	558 mass_mol = data["entry"]["isoforms"][0]["massAsString"]
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	559 seq_length = data['entry']["isoforms"][0]["sequenceLength"]
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	560 iso_elec_point = data['entry']["isoforms"][0]["isoelectricPointAsString"]
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	561 chr_loc = data['entry']["chromosomalLocations"][0]["chromosome"]
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	562 protein_existence = "PE"+str(data['entry']["overview"]['proteinExistence']['level'])
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	563
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	564 #put all subcell loc in a set
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	565 if "subcellular-location" in data['entry']["annotationsByCategory"].keys() :
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	566 subcell_locs = data['entry']["annotationsByCategory"]["subcellular-location"]
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	567 all_subcell_locs = set()
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	568 for loc in subcell_locs :
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	569 all_subcell_locs.add(loc['cvTermName'])
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	570 all_subcell_locs.discard("")
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	571 all_subcell_locs = ";".join(all_subcell_locs)
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	572 else :
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	573 all_subcell_locs = "NA"
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	574
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	575 #put all subcell loc in a set
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	576 if ('disease') in data['entry']['annotationsByCategory'].keys() :
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	577 diseases = data['entry']['annotationsByCategory']['disease']
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	578 all_diseases = set()
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	579 for disease in diseases :
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	580 if (disease['cvTermName'] is not None and disease['cvTermName'] != ""):
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	581 all_diseases.add(disease['cvTermName'])
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	582 if len(all_diseases) > 0 : all_diseases = ";".join(all_diseases)
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	583 else : all_diseases="NA"
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	584 else :
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	585 all_diseases="NA"
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	586
11 ac2cd728c40e planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c proteore parents: 9 diff changeset	587 #get all tm domain
6 f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	588 nb_domains = 0
11 ac2cd728c40e planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c proteore parents: 9 diff changeset	589 if "transmembrane-region" in data['entry']['annotationsByCategory'].keys():
ac2cd728c40e planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c proteore parents: 9 diff changeset	590 tm_domains = data['entry']['annotationsByCategory']["transmembrane-region"]
ac2cd728c40e planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c proteore parents: 9 diff changeset	591 all_tm_domains = set()
ac2cd728c40e planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c proteore parents: 9 diff changeset	592 for tm in tm_domains :
ac2cd728c40e planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c proteore parents: 9 diff changeset	593 all_tm_domains.add(tm['cvTermName'])
ac2cd728c40e planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c proteore parents: 9 diff changeset	594 nb_domains+=1
24 6cbb76823b7b planemo upload commit 3e8aad84b7fe9218370364b1aef3ea5779475f9f-dirty proteore parents: 23 diff changeset	595 #print "nb domains ++"
6cbb76823b7b planemo upload commit 3e8aad84b7fe9218370364b1aef3ea5779475f9f-dirty proteore parents: 23 diff changeset	596 #print (nb_domains)
15 5f39d3ef5fe3 planemo upload commit 45108c8cbeeccab12031bbf6e65f1177222d4e10 proteore parents: 14 diff changeset	597 nextprot_file[:] = []
12 f6afaa1f562c planemo upload commit 39a9e2bf22b07beeca3fb77d86cda25820eb309c-dirty proteore parents: 11 diff changeset	598 nextprot_file.append([id,mass_mol,str(seq_length),iso_elec_point,chr_loc,all_subcell_locs,all_diseases,str(nb_domains),protein_existence])
6 f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	599 writer.writerows(nextprot_file)
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	600
24 6cbb76823b7b planemo upload commit 3e8aad84b7fe9218370364b1aef3ea5779475f9f-dirty proteore parents: 23 diff changeset	601 id = str(10000000000 - int(time.strftime("%Y%m%d")))
6cbb76823b7b planemo upload commit 3e8aad84b7fe9218370364b1aef3ea5779475f9f-dirty proteore parents: 23 diff changeset	602
6cbb76823b7b planemo upload commit 3e8aad84b7fe9218370364b1aef3ea5779475f9f-dirty proteore parents: 23 diff changeset	603 data_table_entry = dict(id=id, release=release_id, name = name, value = path)
6 f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	604 _add_data_table_entry(data_manager_dict, data_table_entry, "proteore_nextprot_ref")
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	605
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	606 #######################################################################################################
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	607 # Main function
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	608 #######################################################################################################
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	609 def main():
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	610 parser = argparse.ArgumentParser()
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	611 parser.add_argument("--hpa", metavar = ("HPA_OPTION"))
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	612 parser.add_argument("--peptideatlas", metavar=("SAMPLE_CATEGORY_ID"))
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	613 parser.add_argument("--id_mapping", metavar = ("ID_MAPPING_SPECIES"))
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	614 parser.add_argument("--interactome", metavar = ("PPI"))
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	615 parser.add_argument("--species")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	616 parser.add_argument("--date")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	617 parser.add_argument("-o", "--output")
6 f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	618 parser.add_argument("--database")
31 faeeabb11a4d "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 30 diff changeset	619 parser.add_argument("--tool_data_path")
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	620 args = parser.parse_args()
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	621
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	622 data_manager_dict = {}
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	623 # Extract json file params
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	624 filename = args.output
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	625 params = from_json_string(open(filename).read())
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	626 target_directory = params[ 'output_data' ][0]['extra_files_path']
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	627 os.mkdir(target_directory)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	628
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	629 ## Download source files from HPA
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	630 try:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	631 hpa = args.hpa
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	632 except NameError:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	633 hpa = None
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	634 if hpa is not None:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	635 #target_directory = "/projet/galaxydev/galaxy/tools/proteore/ProteoRE/tools/resources_building/test-data/"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	636 hpa = hpa.split(",")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	637 for hpa_tissue in hpa:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	638 HPA_sources(data_manager_dict, hpa_tissue, target_directory)
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	639
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	640 ## Download source file from Peptide Atlas query
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	641 try:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	642 peptide_atlas = args.peptideatlas
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	643 date = args.date
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	644 except NameError:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	645 peptide_atlas = None
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	646 if peptide_atlas is not None:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	647 #target_directory = "/projet/galaxydev/galaxy/tools/proteore/ProteoRE/tools/resources_building/test-data/"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	648 peptide_atlas = peptide_atlas.split(",")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	649 for pa_tissue in peptide_atlas:
32 ec1febc6672e "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 31 diff changeset	650 peptide_atlas_sources(data_manager_dict, pa_tissue, date, target_directory)
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	651
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	652 ## Download ID_mapping source file from Uniprot
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	653 try:
40 a7bcc9a0a456 "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 39 diff changeset	654 id_mapping = args.id_mapping
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	655 except NameError:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	656 id_mapping = None
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	657 if id_mapping is not None:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	658 id_mapping = id_mapping .split(",")
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	659 for species in id_mapping :
33 e681d7de4f5e "planemo upload commit ba867b8fa3352695fbda1ae764407f363ee79a50-dirty" proteore parents: 32 diff changeset	660 id_mapping_sources(data_manager_dict, species, target_directory, args.tool_data_path)
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	661
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	662 ## Download PPI ref files from biogrid/bioplex/humap
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	663 try:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	664 interactome=args.interactome
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	665 if interactome == "biogrid" :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	666 species=args.species
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	667 else :
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	668 species="Human"
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	669 except NameError:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	670 interactome=None
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	671 species=None
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	672 if interactome is not None and species is not None:
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	673 PPI_ref_files(data_manager_dict, species, interactome, target_directory)
6 f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	674
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	675 ## Build nextprot ref file for add protein features
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	676 try:
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	677 database=args.database
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	678 except NameError:
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	679 database=None
f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	680 if database is not None :
8 d5badf9de1b0 planemo upload commit 968cd5b4f78f0a1da86fc3bc29f8159f86e199aa-dirty proteore parents: 6 diff changeset	681 Build_nextprot_ref_file(data_manager_dict,target_directory)
6 f281a1eb83d6 planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty proteore parents: 5 diff changeset	682
0 0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	683 #save info to json file
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	684 filename = args.output
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	685 open(filename, 'wb').write(to_json_string(data_manager_dict))
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	686
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	687 if __name__ == "__main__":
0a26460d7366 planemo upload commit dbc027f59706f5b7d3f9f9319f2652baa50e2df5-dirty proteore parents: diff changeset	688 main()

Mercurial > repos > proteore > proteore_data_manager

annotate data_manager/resource_building.py @ 48:09d9fd9b2d8c draft