diff novo_align.py @ 22:482aef16b6f5 draft

planemo upload for repository https://github.com/zipho/novo_align commit 3aa343058f631ac4117c9bc86989dc449f84135f

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/novo_align.py	Thu Jan 25 03:37:56 2018 -0500
@@ -0,0 +1,47 @@
+#!/usr/bin/env python
+from __future__ import print_function
+import argparse
+import shlex
+import os
+import sys
+import logging
+log = logging.getLogger( __name__ )
+
+
+def novo_align(output_filename, index_filename, fwd_file, rev_file ):
+    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)
+    try:
+        os.system(cmdline_str)
+    except:
+        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  # removed old logic here: + "/" + args.index_filename.split("/")[-1]
+    novo_align(args.output_filename, index_file_path, args.forward_filename, args.reverse_filename)
+
+
+if __name__ == "__main__":
+    main()