allpy
changeset 809:b12d3f40a5cb
Added option --pdb-cache to extract_pfam.py
| author | Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru> |
|---|---|
| date | Thu, 14 Jul 2011 16:19:07 +0400 |
| parents | 497de2152849 |
| children | b4edc3eb373b |
| files | utils/extract_pfam.py |
| diffstat | 1 files changed, 5 insertions(+), 2 deletions(-) [+] |
line diff
1.1 --- a/utils/extract_pfam.py Thu Jul 14 16:15:21 2011 +0400 1.2 +++ b/utils/extract_pfam.py Thu Jul 14 16:19:07 2011 +0400 1.3 @@ -26,10 +26,14 @@ 1.4 help='Input file has gzip compression') 1.5 parser.add_option('-G', '--no-gzip', action='store_false', dest='gzip', 1.6 help='Input file is plain text') 1.7 + parser.add_option('-c', '--pdb-cache', default='pdb_cache', 1.8 + help='Directory with PDB files cache') 1.9 options, args = parser.parse_args() 1.10 if options.gzip is None: 1.11 options.gzip = options.infile_name.endswith('.gz') 1.12 options.infile_name = os.path.abspath(options.infile_name) 1.13 + options.pdb_cache = os.path.abspath(options.pdb_cache) 1.14 + download_pdb = structure.CachedDownloadPdb(cache_dir=options.pdb_cache) 1.15 else: 1.16 options = Struct() 1.17 options.min_depth = 2 1.18 @@ -37,8 +41,7 @@ 1.19 options.infile_name = '/srv/databases/pfam/Pfam-A.full.gz' 1.20 options.outdir_name = '/srv/databases/pfam/Pfam-with-PDB' 1.21 options.gzip = True 1.22 - 1.23 -download_pdb = structure.cached_download_pdb 1.24 + download_pdb = structure.cached_download_pdb 1.25 1.26 types = Struct() 1.27 class Monomer(protein.Monomer):