Mercurial > repos > charles_s_test > test_dependencies

annotate testdep.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
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2 import sys, os, io
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3
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4 #input = sys.argv[1]
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5
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6 print(input)
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7
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8 import re, os
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10 def fix_seq_ids(filename):
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11 '''
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12 make sequence ids the same for paired reads.
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13 '''
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14 file = list(open(filename, 'r'))
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15 new_file = open(filename, 'w')
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16 for line in file:
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17 if re.search('^@', line) or re.search('^\+', line) and re.search(' ', line):
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18 linel = re.split(' ', line)
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19 linel[0] = re.sub('.\d$', '', linel[0])
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20 line = ' '.join(linel)
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21 new_file.write(line)
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22 # fastq-dump --log-level fatal --split-3 --accession accession_number --ncbi_error_report never
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23
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24 #os.system('bwa index -a bwtsw /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_454.dat')
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25 os.system('samtools view -bS /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_472.dat > test.bam')
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27 os.system('blastx -query /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_454.dat -out output.blast.txt')
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30 file = open("test.txt","w")
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32 file.write("Hello World")
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34 file.close()
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36 #os.system('/nfs/sw/apps/bwa/bwa-0.7.15/bwa index -a bwtsw /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_454.dat')
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40 #os.system('bwa mem /nfs/sw/apps/galaxy-dev/galaxy/tools/seqsero/database/fliC_b_whole.fasta /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_445.dat /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_446.dat > aln-pe.sam')
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42 #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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44 #os.system('ls -lh | grep ' + input)
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46 #os.system('/nfs/sw/apps/sratoolkit/sratoolkit.2.8.0-centos_linux64/bin/fastq-dump -I --split-files ' + input)
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47 #mv_cmd = 'mv -v ' + input + '_1.fastq R1.fastq'
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48 #print(mv_cmd)
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49
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50 #fix_seq_ids(input + '_1.fastq')
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51 #fix_seq_ids(input + '_2.fastq')
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52
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53 #os.system('mv -v ' + input + '_1.fastq R1.fastq')
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54 #os.system('mv -v ' + input + '_2.fastq R2.fastq')