Mercurial > repos > charles_s_test > test_dependencies

annotate runfastq_dump.py @ 0:500ceb70e4bd draft

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planemo upload commit d4d558b27a09f684be8311f3cfb659b16545e167-dirty
author charles_s_test
date Sun, 12 Nov 2017 09:12:36 -0500
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1 import sys, os
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2
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3 input = sys.argv[1]
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4
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5 print(input)
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6
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7 import re, os
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8
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9 def fix_seq_ids(filename):
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10 '''
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11 make sequence ids the same for paired reads.
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12 '''
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13 file = list(open(filename, 'r'))
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14 new_file = open(filename, 'w')
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15 for line in file:
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16 if re.search('^@', line) or re.search('^\+', line) and re.search(' ', line):
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17 linel = re.split(' ', line)
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18 linel[0] = re.sub('.\d$', '', linel[0])
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19 line = ' '.join(linel)
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20 new_file.write(line)
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21 # fastq-dump --log-level fatal --split-3 --accession accession_number --ncbi_error_report never
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23 os.system('/nfs/sw/apps/sratoolkit/sratoolkit.2.8.0-centos_linux64/bin/fastq-dump --log-level fatal --split-3 --accession ' + input + ' --ncbi_error_report never')
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25 os.system('ls -lh | grep ' + input)
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27 #os.system('/nfs/sw/apps/sratoolkit/sratoolkit.2.8.0-centos_linux64/bin/fastq-dump -I --split-files ' + input)
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28 #mv_cmd = 'mv -v ' + input + '_1.fastq R1.fastq'
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29 #print(mv_cmd)
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31 #fix_seq_ids(input + '_1.fastq')
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32 #fix_seq_ids(input + '_2.fastq')
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34 os.system('mv -v ' + input + '_1.fastq R1.fastq')
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35 os.system('mv -v ' + input + '_2.fastq R2.fastq')
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