changeset 8:e93ae4176127 draft

Uploaded a set of tools

Binary file ._MITObim_1.8.pl has changed

Binary file ._consense.xml has changed

Binary file ._dnapars.xml has changed

Binary file ._interleave-fastqgz-MITOBIM.py has changed

Binary file ._interleave.xml has changed

Binary file ._mitobim.xml has changed

Binary file ._seqboot.xml has changed

--- a/home/lijing/galaxy/tools/ngs_mapping/interleave-fastqgz-MITOBIM.py	Thu Nov 02 12:45:03 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-#!/usr/bin/python
-# encoding:utf8
-# authors: Erik Garrison, Sébastien Boisvert
-# modified by github@cypridina on 20151104 to work with MITObim
-"""This script takes two fastq or fastq.gz files and interleaves them
-Usage:
-    interleave-fasta fasta_file1 fasta_file2
-"""
-
-import sys,re 
-
-def interleave(f1, f2):
-    """Interleaves two (open) fastq files.
-    """
-    while True:
-        line = f1.readline()
-        if line.strip() == "":
-            break
-        print re.sub(r" 1:N.*", "/1",line.strip())
-        
-        for i in xrange(3):
-            print re.sub(r" 2:N.*","/2",f1.readline().strip())
-        
-        for i in xrange(4):
-            print re.sub(r" 2:N.*","/2",f2.readline().strip())
-
-if __name__ == '__main__':
-    try:
-        file1 = sys.argv[1]
-        file2 = sys.argv[2]
-    except:
-        print __doc__
-        sys.exit(1)
-
-    if file1[-2:] == "gz":
-        import gzip
-        with gzip.open(file1) as f1:
-            with gzip.open(file2) as f2:
-                interleave(f1, f2)
-    else:
-        with open(file1) as f1:
-            with open(file2) as f2:
-                interleave(f1, f2)
-    f1.close()
-    f2.close()