# HG changeset patch # User pravs # Date 1528823256 14400 # Node ID 1b61f7aafb617ab51dbdf6f29ee04bf86c2d608d # Parent 561b62936e2cc59ec4115022e17cda811715947b planemo upload diff -r 561b62936e2c -r 1b61f7aafb61 peptideGenomicCoordinate.py --- a/peptideGenomicCoordinate.py Mon Apr 09 16:53:05 2018 -0400 +++ b/peptideGenomicCoordinate.py Tue Jun 12 13:07:36 2018 -0400 @@ -117,9 +117,9 @@ pass if len(spliced_peptide) == 0: if strand == "+": - bed_line = [chromosome, str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "1", str(pep_end-pep_start), "0"] + bed_line = [str(chromosome), str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "1", str(pep_end-pep_start), "0"] else: - bed_line = [chromosome, str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "1", str(pep_end-pep_start), "0"] + bed_line = [str(chromosome), str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "1", str(pep_end-pep_start), "0"] outfh.write("\t".join(bed_line)+"\n") else: if strand == "+": @@ -128,7 +128,7 @@ pep_end = max([pep_entry[0][1], pep_entry[1][1]]) blockSize = [str(min([pep_entry[0][3], pep_entry[1][3]])),str(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]]))] blockStarts = ["0", str(pep_end-pep_start-(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]])))] - bed_line = [chromosome, str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "2", ",".join(blockSize), ",".join(blockStarts)] + bed_line = [str(chromosome), str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "2", ",".join(blockSize), ",".join(blockStarts)] outfh.write("\t".join(bed_line)+"\n") else: pep_entry = spliced_peptide @@ -136,7 +136,7 @@ pep_end = max([pep_entry[0][1], pep_entry[1][1]]) blockSize = [str(min([pep_entry[0][3], pep_entry[1][3]])),str(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]]))] blockStarts = ["0", str(pep_end-pep_start-(max([pep_entry[0][3], pep_entry[1][3]])-min([pep_entry[0][3], pep_entry[1][3]])))] - bed_line = [chromosome, str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "2", ",".join(blockSize), ",".join(blockStarts)] + bed_line = [str(chromosome), str(pep_start), str(pep_end), peptide, "255", strand, str(pep_start), str(pep_end), "0", "2", ",".join(blockSize), ",".join(blockStarts)] outfh.write("\t".join(bed_line)+"\n") c.execute("DROP table novel") conn.commit() diff -r 561b62936e2c -r 1b61f7aafb61 peptideGenomicCoordinate.xml --- a/peptideGenomicCoordinate.xml Mon Apr 09 16:53:05 2018 -0400 +++ b/peptideGenomicCoordinate.xml Tue Jun 12 13:07:36 2018 -0400 @@ -1,4 +1,4 @@ - + Get genomic location/coordinate of peptides using mzsqlite DB and genomic mapping sqlite DB python