Mercurial > repos > earlhaminst > hcluster_sg_parser
changeset 5:07f5b2c5ac10 draft default tip
"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/hcluster_sg_parser commit e015ac3e0d8c1bc62b1301527241ee5e377b91db"
| author | earlhaminst |
|---|---|
| date | Fri, 10 Sep 2021 15:08:06 +0000 |
| parents | 02d73e6ca869 |
| children | |
| files | hcluster_sg_parser.py |
| diffstat | 1 files changed, 7 insertions(+), 1 deletions(-) [+] |
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--- a/hcluster_sg_parser.py Fri Jul 19 11:44:07 2019 -0400 +++ b/hcluster_sg_parser.py Fri Sep 10 15:08:06 2021 +0000 @@ -5,9 +5,10 @@ Usage: -python hcluster_sg_parser.py [-m <N>] [-M <N>] <file> <discarded_out> +python hcluster_sg_parser.py [-m <N>] [-M <N>] <file> <discarded_min_out> <discarded_max_out> """ import optparse +import os import sys @@ -15,8 +16,11 @@ parser = optparse.OptionParser() parser.add_option('-m', '--min', type='int', default=0, help='Minimum number of cluster elements') parser.add_option('-M', '--max', type='int', default=sys.maxsize, help='Maximum number of cluster elements') + parser.add_option('-d', '--dir', type='string', help="Absolute or relative path to output directory. If the directory does not exist, it will be created") options, args = parser.parse_args() + if options.dir and not os.path.exists(options.dir): + os.mkdir(options.dir) with open(args[2], 'w') as discarded_max_out: with open(args[1], 'w') as discarded_min_out: with open(args[0]) as fh: @@ -32,6 +36,8 @@ discarded_max_out.write(id_list) else: outfile = cluster_id + '_output.txt' + if options.dir: + outfile = os.path.join(options.dir, outfile) with open(outfile, 'w') as f: f.write(id_list)