Mercurial > repos > davidvanzessen > mutation_analysis
changeset 50:8ba6afa1247a draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Thu, 28 Jan 2016 09:21:25 -0500 |
| parents | 5c6b9e99d576 |
| children | d4e72eeea640 |
| files | imgt_loader.py imgt_loader.r wrapper.sh |
| diffstat | 3 files changed, 82 insertions(+), 142 deletions(-) [+] |
line wrap: on
line diff
--- a/imgt_loader.py Wed Nov 18 05:55:04 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,141 +0,0 @@ -import pandas as pd -try: - pd.options.mode.chained_assignment = None # default='warn' -except: - pass -import re -import argparse -import os - -def stop_err( msg, ret=1 ): - sys.stderr.write( msg ) - sys.exit( ret ) - -#docs.python.org/dev/library/argparse.html -parser = argparse.ArgumentParser() -parser.add_argument("--summ", help="The 1_Summary file from the imgt output") -parser.add_argument("--aa", help="The 5_AA-Sequence file from the imgt output") -parser.add_argument("--junction", help="The 6_Junction file from the imgt output") -parser.add_argument("--output", help="Output file") - -args = parser.parse_args() - -old_summary_columns = [u'Sequence ID', u'JUNCTION frame', u'V-GENE and allele', u'D-GENE and allele', u'J-GENE and allele', u'CDR1-IMGT length', u'CDR2-IMGT length', u'CDR3-IMGT length', u'Orientation'] -old_sequence_columns = [u'CDR1-IMGT', u'CDR2-IMGT', u'CDR3-IMGT'] -old_junction_columns = [u'JUNCTION'] - -added_summary_columns = [u'Functionality', u'V-REGION identity %', u'V-REGION identity nt', u'D-REGION reading frame', u'AA JUNCTION', u'Functionality comment', u'Sequence'] -added_sequence_columns = [u'FR1-IMGT', u'FR2-IMGT', u'FR3-IMGT', u'CDR3-IMGT', u'JUNCTION', u'J-REGION', u'FR4-IMGT'] -added_junction_columns = [u"P3'V-nt nb", u'N1-REGION-nt nb', u"P5'D-nt nb", u"P3'D-nt nb", u'N2-REGION-nt nb', u"P5'J-nt nb", u"3'V-REGION trimmed-nt nb", u"5'D-REGION trimmed-nt nb", u"3'D-REGION trimmed-nt nb", u"5'J-REGION trimmed-nt nb"] - -outFile = args.output - -#fSummary = pd.read_csv(triplets[0][0], sep="\t", low_memory=False) -fSummary = pd.read_csv(args.summ, sep="\t", dtype=object) -#fSequence = pd.read_csv(triplets[0][1], sep="\t", low_memory=False) -fSequence = pd.read_csv(args.aa, sep="\t", dtype=object) -#fJunction = pd.read_csv(triplets[0][2], sep="\t", low_memory=False) -fJunction = pd.read_csv(args.junction, sep="\t", dtype=object) -tmp = fSummary[["Sequence ID", "JUNCTION frame", "V-GENE and allele", "D-GENE and allele", "J-GENE and allele"]] - -tmp["CDR1 Seq"] = fSequence["CDR1-IMGT"] -tmp["CDR1 Length"] = fSummary["CDR1-IMGT length"] - -tmp["CDR2 Seq"] = fSequence["CDR2-IMGT"] -tmp["CDR2 Length"] = fSummary["CDR2-IMGT length"] - -tmp["CDR3 Seq"] = fSequence["CDR3-IMGT"] -tmp["CDR3 Length"] = fSummary["CDR3-IMGT length"] - -tmp["CDR3 Seq DNA"] = fJunction["JUNCTION"] -tmp["CDR3 Length DNA"] = '1' -tmp["Strand"] = fSummary["Orientation"] -tmp["CDR3 Found How"] = 'a' - -for col in added_summary_columns: - tmp[col] = fSummary[col] - -for col in added_sequence_columns: - tmp[col] = fSequence[col] - -for col in added_junction_columns: - tmp[col] = fJunction[col] - -outFrame = tmp - -outFrame.columns = [u'ID', u'VDJ Frame', u'Top V Gene', u'Top D Gene', u'Top J Gene', u'CDR1 Seq', u'CDR1 Length', u'CDR2 Seq', u'CDR2 Length', u'CDR3 Seq', u'CDR3 Length', u'CDR3 Seq DNA', u'CDR3 Length DNA', u'Strand', u'CDR3 Found How', u'Functionality', 'V-REGION identity %', 'V-REGION identity nt', 'D-REGION reading frame', 'AA JUNCTION', 'Functionality comment', 'Sequence', 'FR1-IMGT', 'FR2-IMGT', 'FR3-IMGT', 'CDR3-IMGT', 'JUNCTION', 'J-REGION', 'FR4-IMGT', 'P3V-nt nb', 'N1-REGION-nt nb', 'P5D-nt nb', 'P3D-nt nb', 'N2-REGION-nt nb', 'P5J-nt nb', '3V-REGION trimmed-nt nb', '5D-REGION trimmed-nt nb', '3D-REGION trimmed-nt nb', '5J-REGION trimmed-nt nb'] - -""" -IGHV[0-9]-[0-9ab]+-?[0-9]?D? -TRBV[0-9]{1,2}-?[0-9]?-?[123]? -IGKV[0-3]D?-[0-9]{1,2} -IGLV[0-9]-[0-9]{1,2} -TRAV[0-9]{1,2}(-[1-46])?(/DV[45678])? -TRGV[234589] -TRDV[1-3] - -IGHD[0-9]-[0-9ab]+ -TRBD[12] -TRDD[1-3] - -IGHJ[1-6] -TRBJ[12]-[1-7] -IGKJ[1-5] -IGLJ[12367] -TRAJ[0-9]{1,2} -TRGJP?[12] -TRDJ[1-4] -""" - -vPattern = [r"(IGHV[0-9]-[0-9ab]+-?[0-9]?D?)", - r"(TRBV[0-9]{1,2}-?[0-9]?-?[123]?)", - r"(IGKV[0-3]D?-[0-9]{1,2})", - r"(IGLV[0-9]-[0-9]{1,2})", - r"(TRAV[0-9]{1,2}(-[1-46])?(/DV[45678])?)", - r"(TRGV[234589])", - r"(TRDV[1-3])"] - -dPattern = [r"(IGHD[0-9]-[0-9ab]+)", - r"(TRBD[12])", - r"(TRDD[1-3])"] - -jPattern = [r"(IGHJ[1-6])", - r"(TRBJ[12]-[1-7])", - r"(IGKJ[1-5])", - r"(IGLJ[12367])", - r"(TRAJ[0-9]{1,2})", - r"(TRGJP?[12])", - r"(TRDJ[1-4])"] - -vPattern = re.compile(r"|".join(vPattern)) - -dPattern = re.compile(r"|".join(dPattern)) - -jPattern = re.compile(r"|".join(jPattern)) - - -def filterGenes(s, pattern): - if type(s) is not str: - return "NA" - res = pattern.search(s) - if res: - return res.group(0) - return "NA" - - - -outFrame["Top V Gene"] = outFrame["Top V Gene"].apply(lambda x: filterGenes(x, vPattern)) -outFrame["Top D Gene"] = outFrame["Top D Gene"].apply(lambda x: filterGenes(x, dPattern)) -outFrame["Top J Gene"] = outFrame["Top J Gene"].apply(lambda x: filterGenes(x, jPattern)) - - -tmp = outFrame["VDJ Frame"] -tmp = tmp.replace("in-frame", "In-frame") -tmp = tmp.replace("null", "Out-of-frame") -tmp = tmp.replace("out-of-frame", "Out-of-frame") -outFrame["VDJ Frame"] = tmp -outFrame["CDR3 Length DNA"] = outFrame["CDR3 Seq DNA"].map(str).map(len) -safeLength = lambda x: len(x) if type(x) == str else 0 -#outFrame = outFrame[(outFrame["CDR3 Seq DNA"].map(safeLength) > 0) & (outFrame["Top V Gene"] != "NA") & (outFrame["Top J Gene"] != "NA")] #filter out weird rows? -#outFrame = outFrame[(outFrame["CDR3 Seq DNA"].map(safeLength) > 0) & (outFrame["Top V Gene"] != "NA") & (outFrame["Top D Gene"] != "NA") & (outFrame["Top J Gene"] != "NA")] #filter out weird rows? -outFrame.to_csv(outFile, sep="\t", index=False, index_label="index")
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/imgt_loader.r Thu Jan 28 09:21:25 2016 -0500 @@ -0,0 +1,80 @@ +args <- commandArgs(trailingOnly = TRUE) + +summ.file = args[1] +aa.file = args[2] +junction.file = args[3] +out.file = args[4] + +summ = read.table(summ.file, sep="\t", header=T, quote="", fill=T) +aa = read.table(aa.file, sep="\t", header=T, quote="", fill=T) +junction = read.table(junction.file, sep="\t", header=T, quote="", fill=T) + +old_summary_columns=c('Sequence.ID','JUNCTION.frame','V.GENE.and.allele','D.GENE.and.allele','J.GENE.and.allele','CDR1.IMGT.length','CDR2.IMGT.length','CDR3.IMGT.length','Orientation') +old_sequence_columns=c('CDR1.IMGT','CDR2.IMGT','CDR3.IMGT') +old_junction_columns=c('JUNCTION') + +added_summary_columns=c('Functionality','V.REGION.identity..','V.REGION.identity.nt','D.REGION.reading.frame','AA.JUNCTION','Functionality.comment','Sequence') +added_sequence_columns=c('FR1.IMGT','FR2.IMGT','FR3.IMGT','CDR3.IMGT','JUNCTION','J.REGION','FR4.IMGT') +added_junction_columns=c("P3.V.nt.nb",'N.REGION.nt.nb','N1.REGION.nt.nb',"P5.D.nt.nb","P3.D.nt.nb",'N2.REGION.nt.nb',"P5.J.nt.nb","X3.V.REGION.trimmed.nt.nb","X5.D.REGION.trimmed.nt.nb","X3.D.REGION.trimmed.nt.nb","X5.J.REGION.trimmed.nt.nb","N.REGION","N1.REGION","N2.REGION") + +out=summ[,c("Sequence.ID","JUNCTION.frame","V.GENE.and.allele","D.GENE.and.allele","J.GENE.and.allele")] + +out[,"CDR1.Seq"] = aa[,"CDR1.IMGT"] +out[,"CDR1.Length"] = summ[,"CDR1.IMGT.length"] + +out[,"CDR2.Seq"] = aa[,"CDR2.IMGT"] +out[,"CDR2.Length"] = summ[,"CDR2.IMGT.length"] + +out[,"CDR3.Seq"] = aa[,"CDR3.IMGT"] +out[,"CDR3.Length"] = summ[,"CDR3.IMGT.length"] + +out[,"CDR3.Seq.DNA"] = junction[,"JUNCTION"] +out[,"CDR3.Length.DNA"] = nchar(as.character(junction[,"JUNCTION"])) +out[,"Strand"] = summ[,"Orientation"] +out[,"CDR3.Found.How"] = "a" + +out[,added_summary_columns] = summ[,added_summary_columns] + +out[,added_sequence_columns] = aa[,added_sequence_columns] + +out[,added_junction_columns] = junction[,added_junction_columns] + +out[,"Top V Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"V.GENE.and.allele"])) +out[,"Top D Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"D.GENE.and.allele"])) +out[,"Top J Gene"] = gsub(".* ", "", gsub("\\*.*", "", summ[,"J.GENE.and.allele"])) + +out = out[,c('Sequence.ID','JUNCTION.frame','Top V Gene','Top D Gene','Top J Gene','CDR1.Seq','CDR1.Length','CDR2.Seq','CDR2.Length','CDR3.Seq','CDR3.Length','CDR3.Seq.DNA','CDR3.Length.DNA','Strand','CDR3.Found.How','Functionality','V.REGION.identity..','V.REGION.identity.nt','D.REGION.reading.frame','AA.JUNCTION','Functionality.comment','Sequence','FR1.IMGT','FR2.IMGT','FR3.IMGT','CDR3.IMGT','JUNCTION','J.REGION','FR4.IMGT','P3.V.nt.nb','N.REGION.nt.nb','N1.REGION.nt.nb','P5.D.nt.nb','P3.D.nt.nb','N2.REGION.nt.nb','P5.J.nt.nb','X3.V.REGION.trimmed.nt.nb','X5.D.REGION.trimmed.nt.nb','X3.D.REGION.trimmed.nt.nb','X5.J.REGION.trimmed.nt.nb','N.REGION','N1.REGION','N2.REGION')] + +names(out) = c('ID','VDJ Frame','Top V Gene','Top D Gene','Top J Gene','CDR1 Seq','CDR1 Length','CDR2 Seq','CDR2 Length','CDR3 Seq','CDR3 Length','CDR3 Seq DNA','CDR3 Length DNA','Strand','CDR3 Found How','Functionality','V-REGION identity %','V-REGION identity nt','D-REGION reading frame','AA JUNCTION','Functionality comment','Sequence','FR1-IMGT','FR2-IMGT','FR3-IMGT','CDR3-IMGT','JUNCTION','J-REGION','FR4-IMGT','P3V-nt nb','N-REGION-nt nb','N1-REGION-nt nb','P5D-nt nb','P3D-nt nb','N2-REGION-nt nb','P5J-nt nb','3V-REGION trimmed-nt nb','5D-REGION trimmed-nt nb','3D-REGION trimmed-nt nb','5J-REGION trimmed-nt nb','N-REGION','N1-REGION','N2-REGION') + +out[,"VDJ Frame"] = as.character(out[,"VDJ Frame"]) + +fltr = out[,"VDJ Frame"] == "in-frame" +if(any(fltr)){ + out[fltr, "VDJ Frame"] = "In-frame" +} + +fltr = out[,"VDJ Frame"] == "null" +if(any(fltr)){ + out[fltr, "VDJ Frame"] = "Out-of-frame" +} + +fltr = out[,"VDJ Frame"] == "out-of-frame" +if(any(fltr)){ + out[fltr, "VDJ Frame"] = "Out-of-frame" +} + +fltr = out[,"VDJ Frame"] == "" +if(any(fltr)){ + out[fltr, "VDJ Frame"] = "Out-of-frame" +} + +for(col in c('Top V Gene','Top D Gene','Top J Gene')){ + out[,col] = as.character(out[,col]) + fltr = out[,col] == "" + if(any(fltr)){ + out[fltr,col] = "NA" + } +} + +write.table(out, out.file, sep="\t", quote=F, row.names=F, col.names=T)
--- a/wrapper.sh Wed Nov 18 05:55:04 2015 -0500 +++ b/wrapper.sh Thu Jan 28 09:21:25 2016 -0500 @@ -147,7 +147,8 @@ if [[ "$naive_output" != "None" ]] then echo "naive_output: $naive_output" - python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output + #python $dir/imgt_loader.py --summ $PWD/summary.txt --aa $PWD/aa.txt --junction $PWD/junction.txt --output $naive_output + Rscript --verbose $dir/imgt_loader.r $PWD/summary.txt $PWD/aa.txt $PWD/junction.txt ${naive_output} 2>&1 Rscript $dir/naive_output.r $naive_output $outdir/merged.txt $naive_output 2>&1 fi