diff interleave-fastqgz-MITOBIM.py @ 6:a03d23c6ab95 draft

MitoBim and interleave

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/interleave-fastqgz-MITOBIM.py	Thu Nov 02 12:44:55 2017 -0400
@@ -0,0 +1,45 @@
+#!/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()