Mercurial > repos > galaxyp > pep_pointer
changeset 2:073a2965e3b2 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer commit e3996c3bda75b16d19997d1e2f67267dd0ea2dff
| author | galaxyp |
|---|---|
| date | Fri, 06 Apr 2018 18:13:10 -0400 |
| parents | dc1b0f54f626 |
| children | a6282baa8c6f |
| files | pep_pointer.py pep_pointer.xml |
| diffstat | 2 files changed, 32 insertions(+), 26 deletions(-) [+] |
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--- a/pep_pointer.py Wed Jan 03 13:55:01 2018 -0500 +++ b/pep_pointer.py Fri Apr 06 18:13:10 2018 -0400 @@ -1,7 +1,7 @@ # # Author: Praveen Kumar -# Updated: Nov 8th, 2017 +# Updated: April 6th, 2018 # # # @@ -38,9 +38,9 @@ start = a[4].strip() end = a[3].strip() else: - print "Something fishy in start end coordinates" + print "Please check the start end coordinates in the GTF file" else: - print "Something fishy in reading" + print "Please check the strand information in the GTF file. It should be '+' or '-'." if not gtf.has_key(strand): gtf[strand] = {} if not gtf[strand].has_key(type): @@ -148,7 +148,7 @@ elif strand == "-": st = "negative" else: - print "Something fishy in writing . . ." + print "Please check the strand information in the GTF file. It should be '+' or '-'." for type in gtf[strand].keys(): data = gtf[strand][type] @@ -162,49 +162,55 @@ # output file outfh = open(inputFile[3], 'w') # outfh = open("classified_1_Mouse_Data_All_peptides_withNewDBs.txt", "w") - + for each in data: - a = each.split("\t") + a = each.strip().split("\t") chr = a[0].strip() - pep_start = a[1].strip() + pep_start = str(int(a[1].strip())+1) pep_end = a[2].strip() strand = a[5].strip() - c.execute("select * from gtf_data where type = 'CDS' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ") - rows = c.fetchall() - if len(rows) > 0: - outfh.write(each.strip() + "\tCDS\n") - else: - c.execute("select * from gtf_data where type = 'five_prime_utr' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ") + each = "\t".join(a[:6]) + if (len(a) == 12 and int(a[9]) == 1) or (len(a) == 6): + c.execute("select * from gtf_data where type = 'CDS' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ") rows = c.fetchall() if len(rows) > 0: - outfh.write(each.strip() + "\tfive_prime_utr\n") + outfh.write(each.strip() + "\tCDS\n") else: - c.execute("select * from gtf_data where type = 'three_prime_utr' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ") + c.execute("select * from gtf_data where type = 'five_prime_utr' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ") rows = c.fetchall() if len(rows) > 0: - outfh.write(each.strip() + "\tthree_prime_utr\n") + outfh.write(each.strip() + "\tfive_prime_utr\n") else: - c.execute("select * from gtf_data where type = 'exon' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ") + c.execute("select * from gtf_data where type = 'three_prime_utr' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ") rows = c.fetchall() if len(rows) > 0: - outfh.write(each.strip() + "\texon\n") + outfh.write(each.strip() + "\tthree_prime_utr\n") else: - c.execute("select * from gtf_data where type = 'intron' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ") + c.execute("select * from gtf_data where type = 'exon' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ") rows = c.fetchall() if len(rows) > 0: - outfh.write(each.strip() + "\tintron\n") + outfh.write(each.strip() + "\texon\n") else: - c.execute("select * from gtf_data where type = 'gene' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ") + c.execute("select * from gtf_data where type = 'intron' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ") rows = c.fetchall() if len(rows) > 0: - outfh.write(each.strip() + "\tgene\n") + outfh.write(each.strip() + "\tintron\n") else: - c.execute("select * from gtf_data where type = 'intergenic' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ") + c.execute("select * from gtf_data where type = 'gene' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ") rows = c.fetchall() if len(rows) > 0: - outfh.write(each.strip() + "\tintergene\n") + outfh.write(each.strip() + "\tgene\n") else: - outfh.write(each.strip() + "\tOVERLAPPING_ON_TWO_REGIONS: PLEASE_LOOK_MANUALLY (Will be updated in next version)\n") + c.execute("select * from gtf_data where type = 'intergenic' and chr = '"+chr+"' and start <= "+pep_start+" and end >= "+pep_end+" and strand = '"+strand+"' ") + rows = c.fetchall() + if len(rows) > 0: + outfh.write(each.strip() + "\tintergene\n") + else: + outfh.write(each.strip() + "\tOVERLAPPING_ON_TWO_REGIONS: PLEASE_LOOK_MANUALLY (Will be updated in next version)\n") + elif (len(a) == 12 and int(a[9]) == 2): + outfh.write(each.strip() + "\tSpliceJunction\n") + else: + outfh.write(each.strip() + "\tPlease check\n") conn.close() outfh.close()
--- a/pep_pointer.xml Wed Jan 03 13:55:01 2018 -0500 +++ b/pep_pointer.xml Fri Apr 06 18:13:10 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="pep_pointer" name="PepPointer" version="0.1.2"> +<tool id="pep_pointer" name="PepPointer" version="0.1.3"> <description>classify genomic location of peptides</description> <requirements> <requirement type="package" version="2.7.9">python</requirement>