diff novo_align.py @ 0:7e0286bd9405 draft

planemo upload for repository https://github.com/zipho/novo_align commit e1bedce305f6cec5dcbc72bc8282665517f902e0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/novo_align.py	Mon Mar 07 08:26:58 2016 -0500
@@ -0,0 +1,54 @@
+#!/usr/bin/env python
+
+from __future__ import print_function
+import argparse
+from subprocess import check_call, CalledProcessError
+from json import load, dump, dumps
+from os import environ, mkdir, makedirs, path
+from os.path import isdir, exists
+import shlex
+import sys
+
+def novo_align(output_directory, index_filename, fwd_file, rev_file ):
+    if exists(output_directory) and not isdir(output_directory):
+        print("Output directory path already exists but is not a directory: {}".format(output_directory),
+              file=sys.stderr)
+    elif not exists(output_directory):
+        mkdir(output_directory)
+
+    #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")
+
+    cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '@RG\tID:readgroup\tPU:platform unit\tLB:library' | samtools view -bS - > {}".format(
+        index_filename,
+        fwd_file,
+        rev_file,
+        output_filename)
+    cmdline = shlex.split(cmdline_str)
+    try:
+        check_call(cmdline)
+    except CalledProcessError:
+        print("Error running the nova-align", file=sys.stderr)
+
+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()
+
+    filename = args.output_filename
+    print("=============================")
+    print(args.__dict__)
+
+    params = load(open(filename, 'rb'))
+    output_directory = params['output_data'][0]['extra_files_path']
+    makedirs(output_directory)
+
+    novo_align(output_directory, args.index_filename, args.forward_filename, args.reverse_filename)
+
+if __name__ == "__main__": main()