diff testdep.py @ 2:aca83a94fd55 draft default tip

planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty

--- a/testdep.py	Sun Nov 12 09:14:07 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-
-import sys, os, io
-
-#input = sys.argv[1]
-
-print(input)
-
-import re, os
-
-def fix_seq_ids(filename):
-        '''
-        make sequence ids the same for paired reads.
-        '''
-        file = list(open(filename, 'r'))
-        new_file = open(filename, 'w')
-        for line in file:
-                if re.search('^@', line) or re.search('^\+', line) and re.search(' ', line):
-                        linel = re.split(' ', line)
-                        linel[0] = re.sub('.\d$', '', linel[0])
-                        line = ' '.join(linel)
-                new_file.write(line)
-# fastq-dump --log-level fatal --split-3 --accession accession_number --ncbi_error_report never
-
-#os.system('bwa index -a bwtsw /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_454.dat')
-os.system('samtools view -bS /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_472.dat > test.bam')
-
-os.system('blastx -query /nfs/sw/apps/galaxy-dev/galaxy/database/files/000/dataset_454.dat -out output.blast.txt')
-
-
-file = open("test.txt","w") 
- 
-file.write("Hello World") 
- 
-file.close() 
-
-#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')
-
-
-
-#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')
-
-#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')
-
-#os.system('ls -lh | grep ' + input)
-
-#os.system('/nfs/sw/apps/sratoolkit/sratoolkit.2.8.0-centos_linux64/bin/fastq-dump -I --split-files ' + input)
-#mv_cmd = 'mv -v ' + input + '_1.fastq R1.fastq'
-#print(mv_cmd)
-
-#fix_seq_ids(input + '_1.fastq')
-#fix_seq_ids(input + '_2.fastq')
-
-#os.system('mv -v ' + input + '_1.fastq R1.fastq')
-#os.system('mv -v ' + input + '_2.fastq R2.fastq')