Mercurial > repos > sanbi-uwc > novo_align
changeset 32:c6e99afd59a8 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc/tree/master/tools/novo_align commit 928e9337a1e33476053e38f1c07247b2306d3209
| author | sanbi-uwc |
|---|---|
| date | Thu, 31 May 2018 03:45:15 -0400 |
| parents | 4d92ef6639a2 |
| children | fc134b9ac951 |
| files | novo_align.py |
| diffstat | 1 files changed, 7 insertions(+), 7 deletions(-) [+] |
line wrap: on
line diff
--- a/novo_align.py Wed May 30 16:30:56 2018 -0400 +++ b/novo_align.py Thu May 31 03:45:15 2018 -0400 @@ -8,14 +8,15 @@ log = logging.getLogger( __name__ ) -def novo_align(output_filename, index_filename, fwd_file, rev_file ): +def novo_align(out_file, out_stats, 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( + cmdline_str = "novoalign -c 8 -k -d {} -f {} {} -i PE 250, 100 -o SAM '{}' 2> {} > {}".format( index_filename, fwd_file, rev_file, param, - output_filename) + out_stats, + out_file) try: os.system(cmdline_str) except: @@ -32,15 +33,14 @@ def main(): parser = argparse.ArgumentParser(description="Generate a BAM file from the Novo Align tool") - parser.add_argument('output_filename') + parser.add_argument('out_file') + parser.add_argument('out_stats') 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) + novo_align(args.out_file, args.out_stats, args.index_filename, args.forward_filename, args.reverse_filename) if __name__ == "__main__":