Package Bio :: Package Align :: Package Applications :: Module _TCoffee
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Source Code for Module Bio.Align.Applications._TCoffee

 1  # Copyright 2009 by Cymon J. Cox and Brad Chapman. All rights reserved. 
 2  # This code is part of the Biopython distribution and governed by its 
 3  # license.  Please see the LICENSE file that should have been included 
 4  # as part of this package. 
 5  """Command line wrapper for the multiple alignment program TCOFFEE. 
 6   
 7  http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html 
 8   
 9  T-Coffee: A novel method for multiple sequence alignments. 
10  Notredame, Higgins, Heringa, JMB,302(205-217) 2000 
11   
12  Last checked against: Version_6.92 
13  """ 
14   
15  import types 
16  from Bio.Application import _Option, _Switch, _Argument, AbstractCommandline 
17   
18 -class TCoffeeCommandline(AbstractCommandline):
19 """Commandline object for the TCoffee alignment program. 20 21 Implements a VERY limited number of options. 22 """ 23 SEQ_TYPES = ["dna","protein","dna_protein"] 24
25 - def __init__(self, cmd="t_coffee", **kwargs):
26 self.parameters = \ 27 [_Option(["-output", "output"], ["output"], 28 None, 29 0, 30 "Specify the output type. " 31 "One (or more separated by a comma) of: " 32 "'clustalw_aln', 'clustalw', 'gcg', 'msf_aln', " 33 "'pir_aln', 'fasta_aln', 'phylip', 'pir_seq', 'fasta_seq'" 34 "Note that biopython will only read clustalw, pir, and fasta", 35 0), 36 _Option(["-infile", "infile"], ["input"], 37 None, 38 1, 39 "Specify the input file.", 40 0,), 41 #Indicates the name of the alignment output by t_coffee. If the 42 #default is used, the alignment is named <your sequences>.aln 43 _Option(["-outfile", "outfile"], ["output"], 44 None, 45 0, 46 "Specify the output file. Default: <your sequences>.aln", 47 0), 48 _Switch(["-convert", "convert"], ["input"], 49 "Specify you want to perform a file conversion"), 50 _Option(["-type"], ["input"], 51 lambda x: x in SEQ_TYPES, 52 0, 53 "Specify the type of sequence being aligned", 54 0), 55 _Option(["-outorder", "outorder"], ["input"], 56 None, 57 0, 58 "Specify the order of sequence to output" 59 "Either 'input', 'aligned' or <filename> of " 60 "Fasta file with sequence order", 61 0), 62 _Option(["-matrix", "matrix"], ["input"], 63 None, 64 0, 65 "Specify the filename of the substitution matrix to use." 66 "Default: blosum62mt", 67 0), 68 _Option(["-gapopen", "gapopen"], ["input"], 69 lambda x: isinstance(x, types.IntType), 70 0, 71 "Indicates the penalty applied for opening a gap " 72 "(negative integer)", 73 0), 74 _Option(["-gapext", "gapext"], ["input"], 75 lambda x: isinstance(x, types.IntType), 76 0, 77 "Indicates the penalty applied for extending a " 78 "gap. (negative integer)", 79 0), 80 _Switch(["-quiet", "quiet"], ["input"], 81 "Turn off log output"), 82 _Option(["-mode", "mode"], ["input"], 83 None, 84 0, 85 "Specifies a special mode: genome, quickaln, dali, 3dcoffee", 86 0) 87 ] 88 AbstractCommandline.__init__(self, cmd, **kwargs)
89