proteore_data_manager: data_manager/resource

annotate data_manager/resource_building.py @ 27:9a400ce8e4e6 draft

planemo upload commit bb113d19d3a756f70784e6a1433902888686ed96-dirty

author	proteore
date	Fri, 17 May 2019 04:09:47 -0400
parents	bf6940ff60a8
children	808c8493ed4f

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

Mercurial > repos > proteore > proteore_data_manager

annotate data_manager/resource_building.py @ 27:9a400ce8e4e6 draft