diff --git a/build.sh b/build.sh new file mode 100644 index 0000000..1ba9b6b --- /dev/null +++ b/build.sh @@ -0,0 +1,4 @@ +mkdir -p "${PREFIX}/share" +cp recognizer.py "${PREFIX}/share" +cp -r resources/* "${PREFIX}/share" +ln -s "${PREFIX}/share/recognizer.py" "${PREFIX}/bin" \ No newline at end of file diff --git a/meta.yaml b/meta.yaml index 242698d..917e58e 100644 --- a/meta.yaml +++ b/meta.yaml @@ -13,7 +13,6 @@ source: build: noarch: generic number: 0 - script: "mkdir -p $PREFIX/bin && cp recognizer.py $PREFIX/bin && cp -r Databases $PREFIX/bin" requirements: run: diff --git a/recognizer.py b/recognizer.py index 8cc5513..4715770 100644 --- a/recognizer.py +++ b/recognizer.py @@ -213,14 +213,6 @@ def cdd2id(blast, cddid=sys.path[0] + '/resources_directory/cddid_all.tbl'): return pd.merge(blast, cddid, left_on='sseqid', right_on='CDD ID', how='left') -def cogblast2protein2cog(cogblast, fun=sys.path[0] + '/resources_directory/fun.tsv', - whog=sys.path[0] + '/resources_directory/cog-20.def.tab'): - fun = pd.read_csv(fun, sep='\t') - whog = parse_whog(whog) - whog = pd.merge(whog, fun, on='COG functional category (letter)', how='left') - return pd.merge(cogblast, whog, on='cog', how='left') - - def pn2database(pn): run_command('makeprofiledb -in {0} -title {1} -out {1}'.format(pn, pn.split('.pn')[0])) @@ -390,7 +382,7 @@ def main(): ncbi_table = pd.read_csv('{}/hmm_PGAP.tsv'.format(args.resources_directory), sep='\t', usecols=[1, 10, 12, 15]) ncbi_table['source_identifier'] = [ide.split('.')[0] for ide in ncbi_table['source_identifier']] ncbi_table['source_identifier'] = ncbi_table['source_identifier'].str.replace('PF', 'pfam') - fun = pd.read_csv('{}/fun.tsv'.format(args.resources_directory), sep='\t') + fun = pd.read_csv('{}/fun.tsv'.format(sys.path[0]), sep='\t') timed_message("Organizing annotation results") blast_cols = ['pident', 'length', 'mismatch', 'gapopen', 'qstart', 'qend', 'sstart', 'send', 'evalue', 'bitscore'] @@ -437,8 +429,7 @@ def main(): report = pd.merge(report, cog_table, left_on='DB ID', right_on='cog', how='left') report.to_csv('{}/COG_report.tsv'.format(args.output), sep='\t', index=False) # cog2ec - report = cog2ec(report, table=args.resources_directory + '/cog2ec.tsv', - resources_dir=args.resources_directory) + report = cog2ec(report, table='{}/cog2ec.tsv'.format(sys.path[0]), resources_dir=args.resources_directory) # cog2ko report = cog2ko(report, cog2ko=args.resources_directory + '/cog2ko.tsv')