diff runfastq_dump.py @ 2:aca83a94fd55 draft default tip

planemo upload commit cd1454c40a43ad9da3d59e6ba8359318fc772c43-dirty

--- a/runfastq_dump.py	Sun Nov 12 09:14:07 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-import sys, os
-
-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('/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')
-
-
-