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fix: run python3 -E to make sure pythonpath is unset
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,78 +1,154 @@ | ||
| import argparse | ||
| from os.path import join | ||
|
|
||
| def _get_counts_file_path(sampledir,s,prog): | ||
| if prog=="circExplorer": | ||
| return join(sampledir,"circExplorer",s+".circExplorer.counts_table.tsv") | ||
| if prog=="circExplorerbwa": | ||
| return join(sampledir,"circExplorer_BWA",s+".circExplorer_bwa.annotation_counts.tsv") | ||
| elif prog=="ciri": | ||
| return join(sampledir,"ciri",s+".ciri.out.filtered") | ||
| elif prog=="dcc": | ||
| return join(sampledir,"DCC",s+".dcc.counts_table.tsv.filtered") | ||
| elif prog=="mapsplice": | ||
| return join(sampledir,"MapSplice",s+".mapsplice.counts_table.tsv.filtered") | ||
| elif prog=="nclscan": | ||
| return join(sampledir,"NCLscan",s+".nclscan.counts_table.tsv.filtered") | ||
| elif prog=="circrnafinder": | ||
| return join(sampledir,"circRNA_finder",s+".circRNA_finder.counts_table.tsv.filtered") | ||
| elif prog=="findcirc": | ||
| return join(sampledir,"find_circ",s+".find_circ.bed.filtered") | ||
|
|
||
| def _get_counts_file_path(sampledir, s, prog): | ||
| if prog == "circExplorer": | ||
| return join(sampledir, "circExplorer", s + ".circExplorer.counts_table.tsv") | ||
| if prog == "circExplorerbwa": | ||
| return join( | ||
| sampledir, "circExplorer_BWA", s + ".circExplorer_bwa.annotation_counts.tsv" | ||
| ) | ||
| elif prog == "ciri": | ||
| return join(sampledir, "ciri", s + ".ciri.out.filtered") | ||
| elif prog == "dcc": | ||
| return join(sampledir, "DCC", s + ".dcc.counts_table.tsv.filtered") | ||
| elif prog == "mapsplice": | ||
| return join(sampledir, "MapSplice", s + ".mapsplice.counts_table.tsv.filtered") | ||
| elif prog == "nclscan": | ||
| return join(sampledir, "NCLscan", s + ".nclscan.counts_table.tsv.filtered") | ||
| elif prog == "circrnafinder": | ||
| return join( | ||
| sampledir, "circRNA_finder", s + ".circRNA_finder.counts_table.tsv.filtered" | ||
| ) | ||
| elif prog == "findcirc": | ||
| return join(sampledir, "find_circ", s + ".find_circ.bed.filtered") | ||
|
|
||
| def main() : | ||
| parser = argparse.ArgumentParser(description='Merge per sample Counts from different circRNA detection tools') | ||
|
|
||
| def main(): | ||
| parser = argparse.ArgumentParser( | ||
| description="Merge per sample Counts from different circRNA detection tools" | ||
| ) | ||
| # INPUTS | ||
| parser.add_argument('--pyscript', dest='pyscript', type=str, required=True, | ||
| help='python script to be run') | ||
| parser.add_argument('--sampledir', dest='sampledir', type=str, required=True, | ||
| help='generally <workdir>/<results>/<sampleName>') | ||
| parser.add_argument('--dcc', dest='dcc', type=int, required=False, default=0, | ||
| help='n_run_dcc') | ||
| parser.add_argument('--mapsplice', dest='mapsplice', type=int, required=False,default=0, | ||
| help='n_run_mapslice') | ||
| parser.add_argument('--findcirc', dest='findcirc', type=int, required=False,default=0, | ||
| help='n_run_findcirc') | ||
| parser.add_argument('--nclscan', dest='nclscan', type=int, required=False,default=0, | ||
| help='n_run_nclscan') | ||
| parser.add_argument('--circrnafinder', dest='circrnafinder', type=int, required=False, default=0, | ||
| help='n_run_circrnafinder') | ||
| parser.add_argument('--samplename', dest='samplename', type=str, required=True, | ||
| help='Sample Name') | ||
| parser.add_argument('--min_read_count_reqd', dest='minreads', type=int, required=False, default=2, | ||
| help='Read count threshold..circRNA with lower than this number of read support are excluded! (default=2)') | ||
| parser.add_argument('--hqcc', dest='hqcc', type=str, required=False, default="circExplorer,circExplorer_bwa", | ||
| help='Comma separated list of high confidence core callers (default="circExplorer,circExplorer_bwa")') | ||
| parser.add_argument('--hqccpn', dest='hqccpn', type=int, required=False, default=1, | ||
| help='Define n:high confidence core callers plus n callers are required to call this circRNA HQ (default 1)') | ||
| parser.add_argument("--reffa",dest="reffa",required=True,type=str, | ||
| help="reference fasta file path") | ||
| parser.add_argument('--pyscriptoutfile',required=True,help='merged table') | ||
| parser.add_argument( | ||
| "--pyscript", | ||
| dest="pyscript", | ||
| type=str, | ||
| required=True, | ||
| help="python script to be run", | ||
| ) | ||
| parser.add_argument( | ||
| "--sampledir", | ||
| dest="sampledir", | ||
| type=str, | ||
| required=True, | ||
| help="generally <workdir>/<results>/<sampleName>", | ||
| ) | ||
| parser.add_argument( | ||
| "--dcc", dest="dcc", type=int, required=False, default=0, help="n_run_dcc" | ||
| ) | ||
| parser.add_argument( | ||
| "--mapsplice", | ||
| dest="mapsplice", | ||
| type=int, | ||
| required=False, | ||
| default=0, | ||
| help="n_run_mapslice", | ||
| ) | ||
| parser.add_argument( | ||
| "--findcirc", | ||
| dest="findcirc", | ||
| type=int, | ||
| required=False, | ||
| default=0, | ||
| help="n_run_findcirc", | ||
| ) | ||
| parser.add_argument( | ||
| "--nclscan", | ||
| dest="nclscan", | ||
| type=int, | ||
| required=False, | ||
| default=0, | ||
| help="n_run_nclscan", | ||
| ) | ||
| parser.add_argument( | ||
| "--circrnafinder", | ||
| dest="circrnafinder", | ||
| type=int, | ||
| required=False, | ||
| default=0, | ||
| help="n_run_circrnafinder", | ||
| ) | ||
| parser.add_argument( | ||
| "--samplename", dest="samplename", type=str, required=True, help="Sample Name" | ||
| ) | ||
| parser.add_argument( | ||
| "--min_read_count_reqd", | ||
| dest="minreads", | ||
| type=int, | ||
| required=False, | ||
| default=2, | ||
| help="Read count threshold..circRNA with lower than this number of read support are excluded! (default=2)", | ||
| ) | ||
| parser.add_argument( | ||
| "--hqcc", | ||
| dest="hqcc", | ||
| type=str, | ||
| required=False, | ||
| default="circExplorer,circExplorer_bwa", | ||
| help='Comma separated list of high confidence core callers (default="circExplorer,circExplorer_bwa")', | ||
| ) | ||
| parser.add_argument( | ||
| "--hqccpn", | ||
| dest="hqccpn", | ||
| type=int, | ||
| required=False, | ||
| default=1, | ||
| help="Define n:high confidence core callers plus n callers are required to call this circRNA HQ (default 1)", | ||
| ) | ||
| parser.add_argument( | ||
| "--reffa", | ||
| dest="reffa", | ||
| required=True, | ||
| type=str, | ||
| help="reference fasta file path", | ||
| ) | ||
| parser.add_argument("--pyscriptoutfile", required=True, help="merged table") | ||
| # OUTPUTS | ||
| parser.add_argument('--outscript',required=True,help='output bash script') | ||
| parser.add_argument("--outscript", required=True, help="output bash script") | ||
| args = parser.parse_args() | ||
|
|
||
| sd=args.sampledir | ||
| sn=args.samplename | ||
| parameters="" | ||
| parameters+=" --circExplorer "+_get_counts_file_path(sd,sn,'circExplorer') | ||
| parameters+=" --ciri "+_get_counts_file_path(sd,sn,'ciri') | ||
| parameters+=" --circExplorerbwa "+_get_counts_file_path(sd,sn,'circExplorerbwa') | ||
| if args.dcc==1: parameters+=" --dcc "+_get_counts_file_path(sd,sn,'dcc') | ||
| if args.mapsplice==1: parameters+=" --mapsplice "+_get_counts_file_path(sd,sn,'mapsplice') | ||
| if args.nclscan==1: parameters+=" --nclscan "+_get_counts_file_path(sd,sn,'nclscan') | ||
| if args.circrnafinder==1: parameters+=" --circrnafinder "+_get_counts_file_path(sd,sn,'circrnafinder') | ||
| if args.findcirc==1: parameters+=" --findcirc "+_get_counts_file_path(sd,sn,'findcirc') | ||
| parameters+=" --reffa "+args.reffa | ||
| parameters+=" --min_read_count_reqd "+str(args.minreads) | ||
| parameters+=" --samplename "+sn | ||
| parameters+=" --hqcc "+args.hqcc | ||
| parameters+=" --hqccpn "+str(args.hqccpn) | ||
| parameters+=" -o "+args.pyscriptoutfile | ||
|
|
||
| with open(args.outscript,'w') as outscript: | ||
| outscript.write("python3 "+args.pyscript+parameters) | ||
|
|
||
| sd = args.sampledir | ||
| sn = args.samplename | ||
| parameters = "" | ||
| parameters += " --circExplorer " + _get_counts_file_path(sd, sn, "circExplorer") | ||
| parameters += " --ciri " + _get_counts_file_path(sd, sn, "ciri") | ||
| parameters += " --circExplorerbwa " + _get_counts_file_path( | ||
| sd, sn, "circExplorerbwa" | ||
| ) | ||
| if args.dcc == 1: | ||
| parameters += " --dcc " + _get_counts_file_path(sd, sn, "dcc") | ||
| if args.mapsplice == 1: | ||
| parameters += " --mapsplice " + _get_counts_file_path(sd, sn, "mapsplice") | ||
| if args.nclscan == 1: | ||
| parameters += " --nclscan " + _get_counts_file_path(sd, sn, "nclscan") | ||
| if args.circrnafinder == 1: | ||
| parameters += " --circrnafinder " + _get_counts_file_path( | ||
| sd, sn, "circrnafinder" | ||
| ) | ||
| if args.findcirc == 1: | ||
| parameters += " --findcirc " + _get_counts_file_path(sd, sn, "findcirc") | ||
| parameters += " --reffa " + args.reffa | ||
| parameters += " --min_read_count_reqd " + str(args.minreads) | ||
| parameters += " --samplename " + sn | ||
| parameters += " --hqcc " + args.hqcc | ||
| parameters += " --hqccpn " + str(args.hqccpn) | ||
| parameters += " -o " + args.pyscriptoutfile | ||
|
|
||
| with open(args.outscript, "w") as outscript: | ||
| outscript.write("python3 -E " + args.pyscript + parameters) | ||
| outscript.close() | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| main() | ||
| main() |