diff novo_align.py @ 5:d51c5af7a8fe draft

planemo upload for repository https://github.com/zipho/novo_align commit c3aee79679931e7a609fea1dade8973c97fb0d21

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/novo_align.py	Fri Mar 11 02:02:09 2016 -0500
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+import argparse
+from subprocess import check_call, CalledProcessError, Popen
+import shlex
+import os
+import logging
+log = logging.getLogger( __name__ )
+
+def novo_align(output_filename, index_filename, fwd_file, rev_file ):
+    #novoalign -c 8 -k -d /cip0/research/ajayi/RNA-seq_Analysis_Project_Case_Study/reference/Homo_Sapiens/out/TB_H37Rv.nix
+    #         -f X165_820L8_.R1_val_1.fq  X165_820L8_.R2_val_2.fq -i PE 250,100
+    #         -o SAM '@RG\tID:readgroup\tPU:platform unit\tLB:library' | samtools view -bS - > `pwd`/out/X165_820L8.bam
+    #output_filename = path.join(output_directory, fwd_file.split(".")[0] + ".bam")
+    param = r'@RG\tID:RG\tSM:$i\tPL:ILLUMINA'
+    cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' | samtools view -bS - > {}".format(
+        index_filename,
+        fwd_file,
+        rev_file,
+        param,
+        output_filename)
+    #cmdline = newSplit(cmdline_str)
+
+    os.system(cmdline_str)
+    #try:
+    #check_call(cmdline)
+    #except CalledProcessError:
+    #    print("Error running the nova-align", file=sys.stderr)
+
+def newSplit(value):
+    lex = shlex.shlex(value)
+    lex.quotes = '"'
+    lex.whitespace_split = True
+    lex.commenters = ''
+    return list(lex)
+
+def main():
+    parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool")
+    parser.add_argument('output_filename')
+    parser.add_argument('--index_filename')
+    parser.add_argument('--forward_filename')
+    parser.add_argument('--reverse_filename')
+    args = parser.parse_args()
+   
+    #a dirty way of referencing the file
+    index_file_path = args.index_filename + "/" + args.index_filename.split("/")[-1]
+    
+    novo_align(args.output_filename, index_file_path, args.forward_filename, args.reverse_filename)
+
+if __name__ == "__main__": main()