Mercurial > repos > charles_s_test > seqsero2

annotate libs/compare_and_change_two_fastq_id.py @ 7:3d6680af0bec draft

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planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Mon, 27 Nov 2017 16:30:27 -0500
parents 6895de35a263
children 53efef402c51
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/env python
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2
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3 import os,sys
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4 file1=sys.argv[1]
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5 file2=sys.argv[2]
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6
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8 def compare_and_change_two_fastq_id(file1,file2):
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9 a=os.popen("head "+file1).read().split("\n")
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10 b=os.popen("head "+file2).read().split("\n")
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11 for x in a:
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12 if x.startswith("@"):
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13 a_title=x.split(" ")[0]
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14 for x in b:
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15 if x.startswith("@"):
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16 b_title=x.split(" ")[0]
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17 if a_title==b_title:
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18 pass
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19 else:
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20 print("changing the title of two seperated fastq files...")
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21 print(a_title,b_title)
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22 os.system("sed "+"-i 's/.1 / /g' "+file1)
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23 print("finished file1")
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24 os.system("sed "+"-i 's/.2 / /g' "+file2)
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25 print("finished file2")
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27 compare_and_change_two_fastq_id(file1,file2)