Mercurial > repos > pravs > peptidegenomiccoordinate

changeset 2:1b61f7aafb61 draft

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planemo upload
author pravs
date Tue, 12 Jun 2018 13:07:36 -0400
parents 561b62936e2c
children 95d606bdfef7
files peptideGenomicCoordinate.py peptideGenomicCoordinate.xml
diffstat 2 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- 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()
--- 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 @@
-<tool id="peptidegenomiccoordinate" name="Peptide Genomic Coordinate" version="0.1.1">
+<tool id="peptidegenomiccoordinate" name="Peptide Genomic Coordinate" version="0.1.2">
     <description>Get genomic location/coordinate of peptides using mzsqlite DB and genomic mapping sqlite DB</description>
     <requirements>
         <requirement type="package" version="2.7.9">python</requirement>