Mercurial > repos > charles_s_test > seqsero

annotate libs/compare_and_change_two_fastq_id.py @ 2:381e1e7109fc draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 464b391afaa5819bc681452e85bea9d882730eb6-dirty
author charles_s_test
date Sun, 12 Nov 2017 02:26:17 -0500
parents 8db411fab3e1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
1 #!/usr/bin/env python
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
2
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
3 import os,sys
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
4 file1=sys.argv[1]
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
5 file2=sys.argv[2]
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
6
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
7
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
8 def compare_and_change_two_fastq_id(file1,file2):
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
9 a=os.popen("head "+file1).read().split("\n")
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
10 b=os.popen("head "+file2).read().split("\n")
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
11 for x in a:
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
12 if x.startswith("@"):
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
13 a_title=x.split(" ")[0]
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
14 for x in b:
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
15 if x.startswith("@"):
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
16 b_title=x.split(" ")[0]
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
17 if a_title==b_title:
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
18 pass
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
19 else:
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
20 print "changing the title of two seperated fastq files..."
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
21 print a_title,b_title
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
22 os.system("sed "+"-i 's/.1 / /g' "+file1)
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
23 print "finished file1"
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
24 os.system("sed "+"-i 's/.2 / /g' "+file2)
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
25 print "finished file2"
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
26
8db411fab3e1 planemo upload commit 844a891e4eaf732830043204ac636907eefb011d-dirty
charles_s_test
parents:
diff changeset
27 compare_and_change_two_fastq_id(file1,file2)