--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/config.py	Thu Dec 19 13:46:43 2019 +0000
@@ -0,0 +1,323 @@
+'''
+All configuration for clustering
+'''
+import os
+import tempfile
+from math import exp
+from collections import namedtuple
+MAIN_DIR = os.path.dirname(os.path.realpath(__file__))
+def add_base_path(base):
+    '''automates generating absolute path in config'''
+    def joined_path(p):
+        '''create absolute path function '''
+        return os.path.join(base, p)
+    return joined_path
+
+PATH = add_base_path(MAIN_DIR)
+
+# clustering general settings
+DIRECTORY_TREE = {'libdir': 'libdir',
+                  'seqclust': 'seqclust',
+                  'assembly': 'seqclust/small_clusters_assembly',
+                  'blastx': 'seqclust/blastx',
+                  'clustering': 'seqclust/clustering',
+                  'clusters': 'seqclust/clustering/clusters',
+                  'superclusters': 'seqclust/clustering/superclusters',
+                  'mgblast': 'seqclust/mgblast',
+                  'blastn': 'seqclust/blastn',
+                  'prerun': 'seqclust/prerun',
+                  'prerun_clusters': 'seqclust/prerun/clusters',
+                  'sequences': 'seqclust/reads',
+                  'custom_databases': 'seqclust/custom_databases'}
+
+if "TEMP" in os.environ:
+    DIRECTORY_TREE['TEMP'] = os.environ["TEMP"]
+else:
+    DIRECTORY_TREE['TEMP'] = tempfile.TemporaryDirectory().name
+
+FILES = {'sample_db': DIRECTORY_TREE['TEMP'] + "/sample.db",
+         'sample_fasta': DIRECTORY_TREE['prerun'] + "/sample.fasta",
+         'prerun_cls_file' : DIRECTORY_TREE['prerun'] + "/sample_hitsort.cls",
+         'filter_sequences_file' : DIRECTORY_TREE['prerun'] + "/filter_sequences.fasta",
+         'sequences_db': DIRECTORY_TREE['TEMP'] + "/sequences.db",
+         'sequences_fasta': DIRECTORY_TREE['sequences'] + "/reads.fasta",
+         'hitsort': DIRECTORY_TREE['clustering'] + "/hitsort",
+         'hitsort_db': DIRECTORY_TREE['TEMP'] + "/hitsort.db",
+         'cls_file': DIRECTORY_TREE['clustering'] + "/hitsort.cls",
+         'clusters_summary_csv': "CLUSTER_TABLE.csv",
+         'profrep_classification_csv': "PROFREP_CLASSIFICATION_TEMPLATE.csv",
+         'superclusters_csv_summary': "SUPERCLUSTER_TABLE.csv",
+         'comparative_analysis_counts_csv': "COMPARATIVE_ANALYSIS_COUNTS.csv",
+         'clusters_info': ".clusters_info.csv",
+         'tarean_report_html': "tarean_report.html",
+         'cluster_report_html' : "cluster_report.html",
+         'supercluster_report_html' : 'supercluster_report.html',
+         'repeat_annotation_summary_rds' : 'repeat_annotation_summary.rds',
+         'summarized_annotation_html' :'summarized_annotation.html',
+         'main_report_html' : 'index.html',
+         'TR_consensus_fasta': "TAREAN_consensus_rank_{}.fasta",
+         'summary_histogram' : 'summary_histogram.png',
+         'comparative_summary_map': 'comparative_summary.png',
+         "how_to_cite" : "HOW_TO_CITE.html",
+         'logfile' : "logfile.txt",
+         'contigs' : "contigs.fasta",
+         'filter_omitted' : DIRECTORY_TREE['sequences'] + "/removed_filtering_positive_reads.fasta",
+         'filter_kept' : DIRECTORY_TREE['sequences'] + "/kept_filtering_positive_reads.fasta"
+}
+
+
+# include in output-  [source, destination]
+INCLUDE = [
+    [PATH("HOW_TO_CITE.html"), FILES["how_to_cite"]]
+]
+
+# this is attribute of path - not a file name!
+FILES_TO_DISCARD_AT_CLEANUP = [
+    'prerun', 'mgblast', 'blastn', "blastx",
+    'hitsort', "repeat_annotation_summary_rds"
+]
+
+# relative links for html files
+HTML_LINKS = {
+    "CLUSTER_TO_SUPERCLUSTER" : "../../superclusters/dir_SC%04d/index.html",
+    "SUPERCLUSTER_TO_CLUSTER" : "../../clusters/dir_CL%04d/index.html",
+    "CLUSTER_TO_CLUSTER" : "../dir_CL%04d/index.html",
+    "SUPERCLUSTER_TO_SUPERCLUSTER" : "../dir_SC%04d/index.html",
+    "CLUSTER_TO_CLUSTER_TABLE" : "../../../../cluster_report.html",
+    "SEPERCLUSTER_TO_CLUSTER_TABLE" : "../../../../cluster_report.html",
+    "ROOT_TO_CLUSTER" : "seqclust/clustering/clusters/dir_CL%04d/index.html",
+    "ROOT_TO_SUPERCLUSTER" : "seqclust/clustering/superclusters/dir_SC%04d/index.html",
+    "ROOT_TO_TAREAN" : "seqclust/clustering/clusters/dir_CL%04d/tarean/report.html",
+    "CLUSTER_TO_KMER_REPORT" : "tarean/report.html",
+    "INDEX_TO_TAREAN": "tarean_report.html",
+    "INDEX_TO_CLUSTER_REPORT": "cluster_report.html",
+    "INDEX_TO_SUPERCLUSTER_REPORT" : "supercluster_report.html",
+    "INDEX_TO_SUMMARIZED_ANNOTATION" : "summarized_annotation.html"
+}
+
+
+EMAX = 42.6  # define how many graph edges can be processed in 1Kb RAM
+# MINIMUM_NUMBER_OF_INPUT_SEQUENCES = 5000
+# FOR TESTING:
+MINIMUM_NUMBER_OF_INPUT_SEQUENCES = 1000
+MINIMUM_NUMBER_OF_READS_IN_CLUSTER = 20  # smaller clusters are not analyzed
+MINIMUM_NUMBER_OF_READS_FOR_MERGING = 20  # smaller clusters will not be merged
+MINIMUM_NUMBER_OF_SHARED_PAIRS_FOR_MERGING = 20  # min size of W param
+
+
+NUMBER_OF_SEQUENCES_FOR_PRERUN_WITH_FILTERING = 50000
+NUMBER_OF_SEQUENCES_FOR_PRERUN_WITHOUT_FILTERING = 20000
+NUMBER_OF_SEQUENCES_FOR_PRERUN = NUMBER_OF_SEQUENCES_FOR_PRERUN_WITHOUT_FILTERING
+CHUNK_SIZE = 20000
+
+
+CLUSTER_EMAX = 2E7  # this parameter higle affect memory usage!
+
+CLUSTER_VMAX = 40000
+SUPERCLUSTER_THRESHOLD = 0.1
+# Number of processors to use - it will be set at runtime
+PROC = None
+RSERVE_PORT = 6311
+
+#some settings related to repeats annotation
+ORF_THRESHOLD = 1200
+PBS_THRESHOLD = 2
+# threshold for rDNA detection - percentage of similarity hits
+RDNA_THRESHOLD = 20
+# threshold for contamination detection
+CONTAMINATION_THRESHOLD = 10
+# tandem ranks codes:
+# 1 : putative tandem repeats - high confidence
+# 2 : putative tandem repeats - low confidence
+# 3 : potential LTR element
+# 4 : rDNA
+TANDEM_RANKS = [1, 2, 3, 4]
+SKIP_CAP3_ASSEMBLY_TANDEM_RANKS = [1]
+FILTER_MIN_PROP_THRESHOLD = 0.03   # this is minimal proportion of graph edges!
+FILTER_MIN_SIZE_THRESHOLD = 1000  # minimal size of the cluster to be consider for filtering
+FILTER_PROPORTION_OF_KEPT = 0.1
+
+R = 'lib'
+# external scripts
+RSOURCE_tarean = PATH('lib/tarean/tarean.R')
+RSOURCE_reporting = PATH('lib/reporting.R')
+RSOURCE_create_annotation = PATH('lib/create_annotation.R')
+LTR_DETECTION = PATH("lib/detect_LTR_insertion_sites.pl")
+
+#PATH to DATABASES:
+DNA_DATABASE = PATH("databases/dna_database_masked.fasta")
+TRNA_DATABASE = PATH("databases/tRNA_database.fasta")
+SATELLITE_MODEL = PATH("databases/satellite_model.rds")
+LASTAL_PARAMS = PATH("databases/lastal_params")
+# for testing
+PROTEIN_DATABASE = None
+CLASSIFICATION_HIERARCHY = None
+CUSTOM_DNA_DATABASE = None
+
+# when modifying this section check if makefile has most recent target for protein database
+PROTEIN_DATABASE_DEFAULT = "VIRIDIPLANTAE3.0"
+PROTEIN_DATABASE_OPTIONS = {'VIRIDIPLANTAE3.0' :
+                            (PATH("databases/protein_database_viridiplantae_v3.0.fasta"),   # change according if you use custom protein database
+                             PATH("databases/classification_tree_viridiplantae_v3.0.rds")),  # classification schem - data.tree object
+                            'VIRIDIPLANTAE2.2' :
+                            (PATH("databases/protein_database_viridiplantae_v2.2.fasta"),   # change according if you use custom protein database
+                             PATH("databases/classification_viridiplantae_tree.rds")),  # classification schem - data.tree object
+                            'METAZOA2.0' :
+                            (PATH("databases/protein_database_metazoa_v3.fasta"), # change according if you use custom protein database
+                             PATH("databases/classification_tree_metazoa_v3.rds")),   # classification schem - data.tree object
+                            'METAZOA3.0' :
+                            (PATH("databases/protein_database_metazoa_v3.fasta"), # change according if you use custom protein database
+                             PATH("databases/classification_tree_metazoa_v3.rds"))   # classification schem - data.tree object
+}
+# if you change PROTEIN_DATABASE_OPTIONS, do not forget to use 'makeblastdb' build blast database
+# and 'diamond makedb' to build diamond database
+
+# PATH to binaries
+LOUVAIN = PATH("louvain")
+BINARIES = PATH("bin")
+
+CAP3_PATTERNS_REPLACE = {"{}.{}.contigs" : [">Contig", ">{}Contig"],
+                         "{}.{}.aln" : ["* Contig", "* {}Contig"],
+                         "{}.{}.contigs.qual" : [">Contig", ">{}Contig"],
+                         "{}.{}.ace" : ["CO Contig", "CO {}Contig"],
+                         "{}.{}.singlets" : None,
+                         "{}.{}.info" : None,
+                         "{}.{}.contigs.links" : None}
+
+CAP3_FILES_MAPPING = {"{}.{}.contigs" : "small_clusters.fasta",
+                      "{}.{}.contigs.qual" : "small_clusters.contigs.qual",
+                      "{}.{}.aln" : "small_clusters.aln",
+                      "{}.{}.ace" : "small_clusters.ace",
+                      "{}.{}.singlets" : None,
+                      "{}.{}.info" : None,
+                      "{}.{}.contigs.links" : None}
+
+CAP3_FILENAMES = list(CAP3_PATTERNS_REPLACE.keys())
+
+CAP3_FILES_GOODNAMES = {"{}.{}.contigs" : "contigs.fasta",
+                        "{}.{}.contigs.qual" : "contigs.qual",
+                        "{}.{}.aln" : "contigs.aln",
+                        "{}.{}.ace" : "contigs.ace",
+                        "{}.{}.singlets" : "singlets.fasta",
+                        "{}.{}.info" : "assembly.info",
+                        "{}.{}.contigs.links" : "contigs.links"}
+
+
+
+
+CAP3_PARAMS = " -p 80 -o 40 " ## not implemented yet
+
+LTR_DETECTION_FILES = {'ADJ': 'LTR_info.ADJ',
+                       'LTR': 'LTR_info.LTR',
+                       'PBS_BLAST': 'LTR_info.with_PBS_blast.csv',
+                       'BASE' : 'LTR_info'}
+
+# options for all-2-all search and annotations
+FilteringThreshod = namedtuple("FilteringThreshold",
+                               "min_lcov min_pid min_ovl min_scov evalue")
+AnnotationParams = namedtuple("AnnotationParams", "blastn blastx blastn_trna")
+Option = namedtuple('Options',
+                    ('name database all2all_search_params filtering_threshold '
+                     'filter_self_hits legacy_database lastdb  annotation_search_params'))
+
+# protein domain search options:
+DIAMOND = {
+    'args': ' -p {max_proc} --max-target-seqs 1 --min-score 30 --freq-sd 1000 --more-sensitive',
+    'output_columns' : "qseqid sseqid qlen slen length ppos bitscore",
+    'column_types' : [str, str, float, float, float, float, float],
+    'program': 'diamond blastx',
+    'filter_function' : lambda x: x.bitscore >= 30,
+    'parallelize' : False
+}
+BLASTX_W3 = {
+    'args': ' -num_alignments 1 -word_size 2 -evalue 0.01 ',
+    'output_columns' : "qseqid sseqid qlen slen length ppos bitscore",
+    'column_types' : [str, str, float, float, float, float, float],
+    'program': 'blastx',
+    'filter_function' : lambda x: x.bitscore >= 33
+}
+BLASTX_W2 = BLASTX_W3
+BLASTX_W2['args'] = ' -num_alignments 1 -word_size 3 -evalue 0.01 '
+
+
+ARGS = None
+
+ILLUMINA = Option(
+    name="illumina",
+    database='blastdb_legacy',
+    all2all_search_params=('mgblast -p 75 -W18 -UT -X40 -KT -JF  -F '
+                           '"m D" -v100000000 -b100000000'
+                           ' -D4 -C 30 -H 30 -i {query} -d {blastdb}'),
+    filtering_threshold=FilteringThreshod(55, 90, 0, 0, 1),
+    filter_self_hits=False,
+    legacy_database=True,
+    lastdb=False,
+    annotation_search_params=AnnotationParams(
+        blastn={
+            'args': ' -task blastn  -num_alignments 1 -evalue 0.01 ',
+            'output_columns' : "qseqid sseqid qlen slen length ppos bitscore",
+            'column_types' : [str, str, float, float, float, float, float],
+            'program': 'blastn',
+            'filter_function' : lambda x: x.length > 30 and x.bitscore > 60
+
+        },
+        blastx=BLASTX_W3,
+        blastn_trna={
+            'args': ' -task blastn  -num_alignments 1 -word_size 7',
+            'output_columns' : "qseqid sseqid qlen slen length ppos bitscore",
+            'column_types' : [str, str, float, float, float, float, float],
+            'program': 'blastn',
+            'filter_function' : lambda x: x.length > 18 and x.bitscore > 60
+        }
+    )
+)
+
+ILLUMINA_DUST_OFF = ILLUMINA._replace(
+    all2all_search_params=('mgblast -p 75 -W18 -UT -X40 -KT -JF  -F '
+                           'F -v100000000 -b100000000'
+                           ' -D4 -C 30 -H 30 -i {query} -d {blastdb}'),
+)
+
+ILLUMINA_SHORT = ILLUMINA._replace(
+    name="illumina_short",
+    all2all_search_params=('mgblast -p 75 -W18 -UT -X40 -KT -JF  -F '
+                           '"m D" -v100000000 -b100000000'
+                           ' -D4 -C 20 -H 30 -i {query} -d {blastdb}'),
+    filtering_threshold=FilteringThreshod(40, 90, 0, 0, 0.1)
+)
+
+
+OXFORD_NANOPORE = Option(
+    name="oxford_nanopore",
+    database='lastdb',
+    all2all_search_params=('last_wrapper.py -f blasttab+ -P1 '
+                           ' -m 700 -p {} '
+                           ' {{blastdb}} {{query}}  ').format(LASTAL_PARAMS),
+    filtering_threshold=FilteringThreshod(40, 50, 0, 0, 0.01),
+    filter_self_hits=True,
+    legacy_database=False,
+    lastdb=True,
+    annotation_search_params=AnnotationParams(
+        blastn={
+            'args': ' -task blastn  -num_alignments 1 -evalue 0.01 -word_size 11',
+            'output_columns' : "qseqid sseqid qlen slen length ppos bitscore",
+            'column_types' : [str, str, float, float, float, float, float],
+            'program': 'blastn',
+            'filter_function' : lambda x: x.length > 30 and x.bitscore > 50
+        },
+        blastx={
+            'args': ' -num_alignments 1 -word_size 2 -evalue 0.1',
+            'output_columns' : "qseqid sseqid qlen slen length ppos bitscore",
+            'column_types' : [str, str, float, float, float, float, float],
+            'program': 'blastx',
+            'filter_function' : lambda x: x.bitscore >= 30
+        },
+        blastn_trna={
+            'args': ' -task blastn  -num_alignments 1 -word_size 7',
+            'output_columns' : "qseqid sseqid qlen slen length ppos bitscore",
+            'column_types' : [str, str, float, float, float, float, float],
+            'program': 'blastn',
+            'filter_function' : lambda x: x.length > 18 and x.length > 60
+        }
+    )
+)