changeset 4:7f94bf630447 draft

interleave

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/home/lijing/galaxy/tools/ngs_mapping/interleave-fastqgz-MITOBIM.py	Thu Nov 02 12:37:35 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() 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/interleave.xml	Thu Nov 02 12:37:35 2017 -0400
@@ -0,0 +1,32 @@
+<tool id="interleave" name="interleave fastqs" version="0.1.0">
+    <description>takes two fastq or fastq.gz files and interleaves them</description>
+    <requirements>
+        <requirement type="package" version="4.0.2">mira4_assembler</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[
+        /home/lijing/galaxy/tools/ngs_mapping/interleave-fastqgz-MITOBIM.py
+        	$fastq1 $fastq2 > $output1
+    ]]></command>
+    <inputs>
+        <param type="data" name="fastq1" format="fastqsanger,fastq" 
+        	   label="Paire end forward read" />
+        <param type="data" name="fastq2" format="fastqsanger,fastq" 
+        	   label="Paire end reverse read" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="fastqsanger" />
+    </outputs>
+
+    <help><![CDATA[
+        
+This script takes two fastq or fastq.gz files and interleaves them
+
+Usage:
+    interleave-fastqgz-MITOBIM.py fastq1 fastq2 > out.fastq
+
+    ]]></help>
+
+</tool>