allpy
changeset 135:8565652a4019
geometrical_core: parser completed
author | boris <bnagaev@gmail.com> |
---|---|
date | Sun, 24 Oct 2010 16:30:44 +0400 |
parents | d2b53635be05 |
children | 6f886484b055 |
files | geometrical_core/geometrical_core.py |
diffstat | 1 files changed, 40 insertions(+), 0 deletions(-) [+] |
line diff
1.1 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 1.2 +++ b/geometrical_core/geometrical_core.py Sun Oct 24 16:30:44 2010 +0400 1.3 @@ -0,0 +1,40 @@ 1.4 +""" 1.5 +Geometrical Core building tool 1.6 +version 2.0 1.7 +""" 1.8 + 1.9 +from allpy.lib import config, project, block 1.10 +Block = block.Block 1.11 +Project = project.Project 1.12 +import argparse 1.13 + 1.14 +r = argparse.FileType('r') 1.15 +w = argparse.FileType('w') 1.16 +c = config 1.17 + 1.18 +p = argparse.ArgumentParser( 1.19 +description='Geometrical Core building tool.', 1.20 +epilog='''1) Distance spreading [angstrom] 1.21 +2) -1 timeout means running Bron-Kerbosh algorithm without timeout 1.22 +3) Alternative core new aa part: read documentation for more information 1.23 +4) Superposition core identifier: main core is 0, first alternative is 1 etc. ''', 1.24 +formatter_class=argparse.ArgumentDefaultsHelpFormatter, 1.25 +#~ argument_default=argparse.SUPPRESS, 1.26 +) 1.27 + 1.28 +p.add_argument('-v','--version',action='version',version='%(prog)s 2.0') 1.29 +p.add_argument('-i',help='Input alignment file',metavar='FILE',type=r,required=True) 1.30 +p.add_argument('-c',help='PDB names conformity file',metavar='FILE',type=r) 1.31 +p.add_argument('-l',help='Output list file',metavar='FILE',type=w) 1.32 +p.add_argument('-f',help='Output fasta file',metavar='FILE',type=w) 1.33 +p.add_argument('-g',help='Output msf file',metavar='FILE',type=w) 1.34 +p.add_argument('-p',help='Output pdb file',metavar='FILE',type=w) 1.35 +p.add_argument('-s',help='Output spt file',metavar='FILE',type=w) 1.36 +p.add_argument('-d',help='Distance spreading',metavar='DELTA',type=float,default=c.delta) 1.37 +p.add_argument('-m',help='Min core size',metavar='MIN_SIZE',type=int,default=c.minsize) 1.38 +p.add_argument('-t',help='Bron-Kerbosh algorithm timeout',type=int,default=c.timeout) 1.39 +p.add_argument('-n',help='Alternative core new aa part',type=float,default=c.ac_new_atoms) 1.40 +p.add_argument('-a',help='Cores count',metavar='NEW_ATOMS',type=int,default=c.ac_count) 1.41 +p.add_argument('-x',help='Superposition core identifier',metavar='SUPER',type=int,default=0) 1.42 + 1.43 +args = p.parse_args()