1.1 --- /dev/null	Thu Jan 01 00:00:00 1970 +0000
     1.2 +++ b/geometrical_core/geometrical-core	Mon Nov 22 13:36:48 2010 +0300
     1.3 @@ -0,0 +1,181 @@
     1.4 +#!/usr/bin/python
     1.5 +"""
     1.6 +Geometrical Core building tool
     1.7 +version 2.0
     1.8 +"""
     1.9 +
    1.10 +from allpy import config, alignment, block
    1.11 +Block = block.Block
    1.12 +Alignment = alignment.Alignment
    1.13 +import argparse
    1.14 +import os
    1.15 +from tempfile import NamedTemporaryFile
    1.16 +
    1.17 +r = argparse.FileType('r')
    1.18 +w = argparse.FileType('w')
    1.19 +c = config
    1.20 +
    1.21 +def f_nng(string):
    1.22 +    """ Validates nonnegative (>=0) float """
    1.23 +    try:
    1.24 +        value = float(string)
    1.25 +    except:
    1.26 +        msg = "%r is wrong float" % string
    1.27 +        raise argparse.ArgumentTypeError(msg)
    1.28 +    if value < 0:
    1.29 +        msg = "%r is negative" % string
    1.30 +        raise argparse.ArgumentTypeError(msg)
    1.31 +    return value
    1.32 +
    1.33 +def part(string):
    1.34 +    """ Validates 0.0 <= float <= 1.0 """
    1.35 +    try:
    1.36 +        value = float(string)
    1.37 +    except:
    1.38 +        msg = "%r is wrong float" % string
    1.39 +        raise argparse.ArgumentTypeError(msg)
    1.40 +    if not (0.0 <= value <= 1.0):
    1.41 +        msg = "%r is not float, representing part, ie in [0, 1]" % string
    1.42 +        raise argparse.ArgumentTypeError(msg)
    1.43 +    return value
    1.44 +
    1.45 +def timeout(string):
    1.46 +    """ Validates int >= -1 """
    1.47 +    try:
    1.48 +        value = int(string)
    1.49 +    except:
    1.50 +        msg = "%r is wrong integer" % string
    1.51 +        raise argparse.ArgumentTypeError(msg)
    1.52 +    if value < -1:
    1.53 +        msg = "integer %r is less than -1" % string
    1.54 +        raise argparse.ArgumentTypeError(msg)
    1.55 +    return value
    1.56 +
    1.57 +def pos(string):
    1.58 +    """ Validates positive integer """
    1.59 +    try:
    1.60 +        value = int(string)
    1.61 +    except:
    1.62 +        msg = "%r is wrong integer" % string
    1.63 +        raise argparse.ArgumentTypeError(msg)
    1.64 +    if value < 1:
    1.65 +        msg = "%r is not positive integer" % string
    1.66 +        raise argparse.ArgumentTypeError(msg)
    1.67 +    return value
    1.68 +
    1.69 +def i_nng(string):
    1.70 +    """ Validates int >= 0 """
    1.71 +    try:
    1.72 +        value = int(string)
    1.73 +    except:
    1.74 +        msg = "%r is wrong integer" % string
    1.75 +        raise argparse.ArgumentTypeError(msg)
    1.76 +    if value < 0:
    1.77 +        msg = "integer %r is less than 0" % string
    1.78 +        raise argparse.ArgumentTypeError(msg)
    1.79 +    return value
    1.80 +
    1.81 +p = argparse.ArgumentParser(
    1.82 +description='Geometrical Core building tool.',
    1.83 +epilog='''1) Distance spreading [angstrom]
    1.84 +2) -1 timeout means running Bron-Kerbosh algorithm without timeout
    1.85 +3) Alternative core new aa part: read documentation for more information
    1.86 +4) Superposition core identifier: main core is 0, first alternative is 1 etc. ''',
    1.87 +formatter_class=argparse.ArgumentDefaultsHelpFormatter, 
    1.88 +#~ argument_default=argparse.SUPPRESS,
    1.89 +)
    1.90 +
    1.91 +p.add_argument('-v','--version',action='version',version='%(prog)s 2.0')
    1.92 +p.add_argument('-i',help='Input alignment file',metavar='FILE',type=r,required=True)
    1.93 +p.add_argument('-c',help='PDB names conformity file',metavar='FILE',type=r)
    1.94 +p.add_argument('-l',help='Output list file',metavar='FILE',type=w)
    1.95 +p.add_argument('-f',help='Output fasta file',metavar='FILE',type=w)
    1.96 +p.add_argument('-g',help='Output msf file',metavar='FILE',type=w)
    1.97 +p.add_argument('-p',help='Output pdb file',metavar='FILE',type=w)
    1.98 +p.add_argument('-s',help='Output spt file',metavar='FILE',type=w)
    1.99 +p.add_argument('-d',help='Distance spreading',metavar='DELTA',type=f_nng,default=c.delta)
   1.100 +p.add_argument('-m',help='Min core size',metavar='MIN_SIZE',type=pos,default=c.minsize)
   1.101 +p.add_argument('-t',help='Bron-Kerbosh algorithm timeout',type=timeout,default=c.timeout)
   1.102 +p.add_argument('-n',help='Alternative core new aa part',type=part,default=c.ac_new_atoms)
   1.103 +p.add_argument('-a',help='Cores count',metavar='NEW_ATOMS',type=pos,default=c.ac_count)
   1.104 +p.add_argument('-x',help='Superposition core identifier',type=i_nng,default=0)
   1.105 +
   1.106 +tmp_file = None
   1.107 +
   1.108 +try:
   1.109 +    args = p.parse_args()
   1.110 +    
   1.111 +    if not args.l and not args.f and not args.g and not args.p and not args.s:
   1.112 +        print 'Error: no output file provided'
   1.113 +        exit()
   1.114 +    if not (args.p and args.s) and not (not args.p and not args.s):
   1.115 +        print 'Error: provide both pdb and spt file or none of them'
   1.116 +        exit()
   1.117 +    
   1.118 +    try:
   1.119 +        alignment = Alignment(args.i)
   1.120 +    except:
   1.121 +        args.i.close()
   1.122 +        tmp_file = NamedTemporaryFile(delete=False)
   1.123 +        tmp_file.close()
   1.124 +        os.system('seqret %(msf)s %(fasta)s' % \
   1.125 +        {'msf': args.i.name, 'fasta': tmp_file.name})
   1.126 +        args.i = open(tmp_file.name)
   1.127 +        alignment = Alignment(args.i)
   1.128 +    
   1.129 +    block = Block(alignment)
   1.130 +    GCs = block.geometrical_cores(max_delta=args.d, timeout=args.t, 
   1.131 +        minsize=args.t, ac_new_atoms=args.n, ac_count=args.a)
   1.132 +    
   1.133 +    if not GCs:
   1.134 +        print 'No cores! Try to change parameters'
   1.135 +        exit()
   1.136 +    
   1.137 +    if args.l:
   1.138 +        l = args.l
   1.139 +        
   1.140 +        l.write('Geometrical core positions for alignment %s' % args.i.name)
   1.141 +        l.write('\n\n')
   1.142 +        l.write('First alignment position is 0')
   1.143 +        
   1.144 +        for i, GC in enumerate(GCs):
   1.145 +            l.write('\n\n')
   1.146 +            if i == 0:
   1.147 +                l.write('Geometrical core:')
   1.148 +            else:
   1.149 +                l.write('Alternative geometrical core %i:' % i)
   1.150 +            l.write('\n')
   1.151 +            l.write(', '.join(str(n) for n in GC.positions))
   1.152 +        l.close()
   1.153 +    
   1.154 +    if args.g and not args.f:
   1.155 +        args.f = args.g
   1.156 +    
   1.157 +    if args.f:
   1.158 +        args.i.seek(0)
   1.159 +        f = args.f
   1.160 +        f.write(args.i.read()) # write sequences
   1.161 +        
   1.162 +        # write GCs
   1.163 +        for i, GC in enumerate(GCs):
   1.164 +            f.write('\n\n')
   1.165 +            if i == 0:
   1.166 +                GC.save_xstring(f, 'GC', 'Main geometrical core')
   1.167 +            else:
   1.168 +                GC.save_xstring(f, 'AGC_%i' % i, 'Alternative geometrical core %i' % i)
   1.169 +        f.close()
   1.170 +
   1.171 +        
   1.172 +    if args.g:
   1.173 +        args.g.close()
   1.174 +        os.system('seqret %(fasta)s msf::%(msf)s' % \
   1.175 +        {'fasta': args.f.name, 'msf': args.g.name})
   1.176 +    
   1.177 +    
   1.178 +except Exception, t:
   1.179 +    print t
   1.180 +    exit()
   1.181 +
   1.182 +if tmp_file:
   1.183 +    os.unlink(tmp_file)
   1.184 +

     2.1 --- a/geometrical_core/geometrical_core.py	Fri Nov 19 00:17:11 2010 +0300
     2.2 +++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
     2.3 @@ -1,180 +0,0 @@
     2.4 -"""
     2.5 -Geometrical Core building tool
     2.6 -version 2.0
     2.7 -"""
     2.8 -
     2.9 -from allpy import config, alignment, block
    2.10 -Block = block.Block
    2.11 -Alignment = alignment.Alignment
    2.12 -import argparse
    2.13 -import os
    2.14 -from tempfile import NamedTemporaryFile
    2.15 -
    2.16 -r = argparse.FileType('r')
    2.17 -w = argparse.FileType('w')
    2.18 -c = config
    2.19 -
    2.20 -def f_nng(string):
    2.21 -    """ Validates nonnegative (>=0) float """
    2.22 -    try:
    2.23 -        value = float(string)
    2.24 -    except:
    2.25 -        msg = "%r is wrong float" % string
    2.26 -        raise argparse.ArgumentTypeError(msg)
    2.27 -    if value < 0:
    2.28 -        msg = "%r is negative" % string
    2.29 -        raise argparse.ArgumentTypeError(msg)
    2.30 -    return value
    2.31 -
    2.32 -def part(string):
    2.33 -    """ Validates 0.0 <= float <= 1.0 """
    2.34 -    try:
    2.35 -        value = float(string)
    2.36 -    except:
    2.37 -        msg = "%r is wrong float" % string
    2.38 -        raise argparse.ArgumentTypeError(msg)
    2.39 -    if not (0.0 <= value <= 1.0):
    2.40 -        msg = "%r is not float, representing part, ie in [0, 1]" % string
    2.41 -        raise argparse.ArgumentTypeError(msg)
    2.42 -    return value
    2.43 -
    2.44 -def timeout(string):
    2.45 -    """ Validates int >= -1 """
    2.46 -    try:
    2.47 -        value = int(string)
    2.48 -    except:
    2.49 -        msg = "%r is wrong integer" % string
    2.50 -        raise argparse.ArgumentTypeError(msg)
    2.51 -    if value < -1:
    2.52 -        msg = "integer %r is less than -1" % string
    2.53 -        raise argparse.ArgumentTypeError(msg)
    2.54 -    return value
    2.55 -
    2.56 -def pos(string):
    2.57 -    """ Validates positive integer """
    2.58 -    try:
    2.59 -        value = int(string)
    2.60 -    except:
    2.61 -        msg = "%r is wrong integer" % string
    2.62 -        raise argparse.ArgumentTypeError(msg)
    2.63 -    if value < 1:
    2.64 -        msg = "%r is not positive integer" % string
    2.65 -        raise argparse.ArgumentTypeError(msg)
    2.66 -    return value
    2.67 -
    2.68 -def i_nng(string):
    2.69 -    """ Validates int >= 0 """
    2.70 -    try:
    2.71 -        value = int(string)
    2.72 -    except:
    2.73 -        msg = "%r is wrong integer" % string
    2.74 -        raise argparse.ArgumentTypeError(msg)
    2.75 -    if value < 0:
    2.76 -        msg = "integer %r is less than 0" % string
    2.77 -        raise argparse.ArgumentTypeError(msg)
    2.78 -    return value
    2.79 -
    2.80 -p = argparse.ArgumentParser(
    2.81 -description='Geometrical Core building tool.',
    2.82 -epilog='''1) Distance spreading [angstrom]
    2.83 -2) -1 timeout means running Bron-Kerbosh algorithm without timeout
    2.84 -3) Alternative core new aa part: read documentation for more information
    2.85 -4) Superposition core identifier: main core is 0, first alternative is 1 etc. ''',
    2.86 -formatter_class=argparse.ArgumentDefaultsHelpFormatter, 
    2.87 -#~ argument_default=argparse.SUPPRESS,
    2.88 -)
    2.89 -
    2.90 -p.add_argument('-v','--version',action='version',version='%(prog)s 2.0')
    2.91 -p.add_argument('-i',help='Input alignment file',metavar='FILE',type=r,required=True)
    2.92 -p.add_argument('-c',help='PDB names conformity file',metavar='FILE',type=r)
    2.93 -p.add_argument('-l',help='Output list file',metavar='FILE',type=w)
    2.94 -p.add_argument('-f',help='Output fasta file',metavar='FILE',type=w)
    2.95 -p.add_argument('-g',help='Output msf file',metavar='FILE',type=w)
    2.96 -p.add_argument('-p',help='Output pdb file',metavar='FILE',type=w)
    2.97 -p.add_argument('-s',help='Output spt file',metavar='FILE',type=w)
    2.98 -p.add_argument('-d',help='Distance spreading',metavar='DELTA',type=f_nng,default=c.delta)
    2.99 -p.add_argument('-m',help='Min core size',metavar='MIN_SIZE',type=pos,default=c.minsize)
   2.100 -p.add_argument('-t',help='Bron-Kerbosh algorithm timeout',type=timeout,default=c.timeout)
   2.101 -p.add_argument('-n',help='Alternative core new aa part',type=part,default=c.ac_new_atoms)
   2.102 -p.add_argument('-a',help='Cores count',metavar='NEW_ATOMS',type=pos,default=c.ac_count)
   2.103 -p.add_argument('-x',help='Superposition core identifier',type=i_nng,default=0)
   2.104 -
   2.105 -tmp_file = None
   2.106 -
   2.107 -try:
   2.108 -    args = p.parse_args()
   2.109 -    
   2.110 -    if not args.l and not args.f and not args.g and not args.p and not args.s:
   2.111 -        print 'Error: no output file provided'
   2.112 -        exit()
   2.113 -    if not (args.p and args.s) and not (not args.p and not args.s):
   2.114 -        print 'Error: provide both pdb and spt file or none of them'
   2.115 -        exit()
   2.116 -    
   2.117 -    try:
   2.118 -        alignment = Alignment(args.i)
   2.119 -    except:
   2.120 -        args.i.close()
   2.121 -        tmp_file = NamedTemporaryFile(delete=False)
   2.122 -        tmp_file.close()
   2.123 -        os.system('seqret %(msf)s %(fasta)s' % \
   2.124 -        {'msf': args.i.name, 'fasta': tmp_file.name})
   2.125 -        args.i = open(tmp_file.name)
   2.126 -        alignment = Alignment(args.i)
   2.127 -    
   2.128 -    block = Block(alignment)
   2.129 -    GCs = block.geometrical_cores(max_delta=args.d, timeout=args.t, 
   2.130 -        minsize=args.t, ac_new_atoms=args.n, ac_count=args.a)
   2.131 -    
   2.132 -    if not GCs:
   2.133 -        print 'No cores! Try to change parameters'
   2.134 -        exit()
   2.135 -    
   2.136 -    if args.l:
   2.137 -        l = args.l
   2.138 -        
   2.139 -        l.write('Geometrical core positions for alignment %s' % args.i.name)
   2.140 -        l.write('\n\n')
   2.141 -        l.write('First alignment position is 0')
   2.142 -        
   2.143 -        for i, GC in enumerate(GCs):
   2.144 -            l.write('\n\n')
   2.145 -            if i == 0:
   2.146 -                l.write('Geometrical core:')
   2.147 -            else:
   2.148 -                l.write('Alternative geometrical core %i:' % i)
   2.149 -            l.write('\n')
   2.150 -            l.write(', '.join(str(n) for n in GC.positions))
   2.151 -        l.close()
   2.152 -    
   2.153 -    if args.g and not args.f:
   2.154 -        args.f = args.g
   2.155 -    
   2.156 -    if args.f:
   2.157 -        args.i.seek(0)
   2.158 -        f = args.f
   2.159 -        f.write(args.i.read()) # write sequences
   2.160 -        
   2.161 -        # write GCs
   2.162 -        for i, GC in enumerate(GCs):
   2.163 -            f.write('\n\n')
   2.164 -            if i == 0:
   2.165 -                GC.save_xstring(f, 'GC', 'Main geometrical core')
   2.166 -            else:
   2.167 -                GC.save_xstring(f, 'AGC_%i' % i, 'Alternative geometrical core %i' % i)
   2.168 -        f.close()
   2.169 -
   2.170 -        
   2.171 -    if args.g:
   2.172 -        args.g.close()
   2.173 -        os.system('seqret %(fasta)s msf::%(msf)s' % \
   2.174 -        {'fasta': args.f.name, 'msf': args.g.name})
   2.175 -    
   2.176 -    
   2.177 -except Exception, t:
   2.178 -    print t
   2.179 -    exit()
   2.180 -
   2.181 -if tmp_file:
   2.182 -    os.unlink(tmp_file)
   2.183 -