Mercurial > repos > drosofff > mir_parser
changeset 1:101fec3cba04 draft
planemo upload for repository https://bitbucket.org/drosofff/gedtools/
| author | drosofff |
|---|---|
| date | Thu, 13 Aug 2015 06:16:29 -0400 |
| parents | 035df35a257e |
| children | c68bfbff72d5 |
| files | MirParser.py |
| diffstat | 1 files changed, 62 insertions(+), 44 deletions(-) [+] |
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--- a/MirParser.py Mon Jun 29 05:50:44 2015 -0400 +++ b/MirParser.py Thu Aug 13 06:16:29 2015 -0400 @@ -5,77 +5,95 @@ # <6:pathToLatticeDataframe or "dummy_dataframe_path"> <7:Rcode or "dummy_plotCode"> <8:latticePDF or "dummy_latticePDF"> # <9:10:11 filePath:FileExt:FileLabel> <.. ad lib> -import sys, subprocess +import sys +import subprocess + from smRtools import * IndexSource = sys.argv[1] ExtractionDirective = sys.argv[2] if ExtractionDirective == "--do_not_extract_index": - genomeRefFormat = "fastaSource" -elif ExtractionDirective == "--extract_index": - genomeRefFormat = "bowtieIndex" + genomeRefFormat = "fastaSource" +elif ExtractionDirective == "--extract_index": + genomeRefFormat = "bowtieIndex" OutputPre_mirs = sys.argv[3] OutputMature_Mirs = sys.argv[4] GFF3_file = sys.argv[5] lattice = sys.argv[6] Rcode = sys.argv[7] latticePDF = sys.argv[8] -Triplets = [sys.argv[9:][i:i+3] for i in xrange(0, len(sys.argv[9:]), 3)] +Triplets = [sys.argv[9:][i:i + 3] for i in xrange(0, len(sys.argv[9:]), 3)] MasterListOfGenomes = {} for [filePath, FileExt, FileLabel] in Triplets: - print FileLabel - MasterListOfGenomes[FileLabel] = HandleSmRNAwindows (alignmentFile=filePath, alignmentFileFormat=FileExt, genomeRefFile=IndexSource, genomeRefFormat=genomeRefFormat, biosample=FileLabel) + print FileLabel + MasterListOfGenomes[FileLabel] = HandleSmRNAwindows(alignmentFile=filePath, + alignmentFileFormat=FileExt, + genomeRefFile=IndexSource, + genomeRefFormat=genomeRefFormat, + biosample=FileLabel) header = ["gene"] for [filePath, FileExt, FileLabel] in Triplets: - header.append(FileLabel) + header.append(FileLabel) -hit_table = ["\t".join(header)] # table header: gene, sample1, sample2, sample3, etc. separated by tabulation +hit_table = ["\t".join(header)] # table header: gene, sample1, sample2, sample3, etc. separated by tabulation -## read GFF3 to subinstantiate -gff3 = open (GFF3_file, "r") +# read GFF3 to subinstantiate +gff3 = open(GFF3_file, "r") lattice_dataframe = [] for line in gff3: - if line[0] == "#": continue - gff_fields = line[:-1].split("\t") - chrom = gff_fields[0] - gff_name = gff_fields[-1].split("Name=")[-1].split(";")[0] # to isolate the GFF Name - item_upstream_coordinate = int(gff_fields[3]) - item_downstream_coordinate = int(gff_fields[4]) - if gff_fields[6] == "+": - item_polarity = "forward" - else: - item_polarity = "reverse" - item_line = [gff_name] - for sample in header[1:]: - count = MasterListOfGenomes[sample].instanceDict[chrom].readcount(upstream_coord=item_upstream_coordinate, downstream_coord=item_downstream_coordinate, polarity=item_polarity) - item_line.append(str(count)) - ## subtreatement for lattice - if lattice != "dummy_dataframe_path": - if ("5p" not in gff_name) and ("3p" not in gff_name): - lattice_dataframe.append(MasterListOfGenomes[sample].instanceDict[chrom].readcoverage(upstream_coord=item_upstream_coordinate, downstream_coord=item_downstream_coordinate, windowName=gff_name+"_"+sample) ) - ## end of subtreatement for lattice - hit_table.append("\t".join(item_line) ) + if line[0] == "#": + continue + gff_fields = line[:-1].split("\t") + chrom = gff_fields[0] + gff_name = gff_fields[-1].split("Name=")[-1].split(";")[0] # to isolate the GFF Name + item_upstream_coordinate = int(gff_fields[3]) + item_downstream_coordinate = int(gff_fields[4]) + if gff_fields[6] == "+": + item_polarity = "forward" + else: + item_polarity = "reverse" + item_line = [gff_name] + for sample in header[1:]: + count = MasterListOfGenomes[sample].instanceDict[chrom].readcount(upstream_coord=item_upstream_coordinate, + downstream_coord=item_downstream_coordinate, + polarity=item_polarity) + item_line.append(str(count)) + # subtreatement for lattice + if lattice != "dummy_dataframe_path": + if ("5p" not in gff_name) and ("3p" not in gff_name): + lattice_dataframe.append(MasterListOfGenomes[sample].instanceDict[chrom].readcoverage( + upstream_coord=item_upstream_coordinate, + downstream_coord=item_downstream_coordinate, + windowName=gff_name + "_" + sample)) + # end of subtreatement for lattice + hit_table.append("\t".join(item_line)) gff3.close() -Fpremirs = open (OutputPre_mirs, "w") +Fpremirs = open(OutputPre_mirs, "w") print >> Fpremirs, hit_table[0] -finalPreList = [ i for i in sorted(hit_table[1:]) if ("5p" not in i) and ("3p" not in i)] -print >> Fpremirs, "\n".join(finalPreList ) +finalPreList = [i for i in sorted(hit_table[1:]) if ("5p" not in i) and ("3p" not in i)] +print >> Fpremirs, "\n".join(finalPreList) Fpremirs.close() -Fmaturemires = open (OutputMature_Mirs, "w") +Fmaturemires = open(OutputMature_Mirs, "w") print >> Fmaturemires, hit_table[0] -finalMatureList = [ i for i in sorted(hit_table[1:]) if ("5p" in i) or ("3p" in i)] -print >> Fmaturemires, "\n".join(finalMatureList ) +finalMatureList = [i for i in sorted(hit_table[1:]) if ("5p" in i) or ("3p" in i)] +print >> Fmaturemires, "\n".join(finalMatureList) Fmaturemires.close() if lattice != "dummy_dataframe_path": - Flattice = open(lattice, "w") - print >> Flattice, "%s\t%s\t%s\t%s\t%s\t%s\t%s" % ("sample", "mir", "offset", "offsetNorm", "counts","countsNorm", "polarity") - print >> Flattice, "\n".join(lattice_dataframe) - Flattice.close() - R_command="Rscript "+ Rcode - process = subprocess.Popen(R_command.split()) - process.wait() + Flattice = open(lattice, "w") + print >> Flattice, "%s\t%s\t%s\t%s\t%s\t%s\t%s" % ("sample", + "mir", + "offset", + "offsetNorm", + "counts", + "countsNorm", + "polarity") + print >> Flattice, "\n".join(lattice_dataframe) + Flattice.close() + R_command = "Rscript " + Rcode + process = subprocess.Popen(R_command.split()) + process.wait()