Package Bio :: Package Align :: Package Applications :: Module _Probcons
[hide private]
[frames] | no frames]

Source Code for Module Bio.Align.Applications._Probcons

 1  # Copyright 2009 by Cymon J. Cox.  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 PROBCONS. 
 6   
 7  http://probcons.stanford.edu/ 
 8   
 9  Citations: 
10  Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: 
11  Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 
12  330-340.  
13   
14  Last checked agains version: 1.12 
15  """ 
16  import types 
17  from Bio.Application import _Option, _Switch, _Argument, AbstractCommandline 
18   
19 -class ProbconsCommandline(AbstractCommandline):
20 """Command line wrapper for the multiple alignment program PROBCONS."""
21 - def __init__(self, cmd="probcons", **kwargs):
22 self.parameters = \ 23 [ 24 #Note that some options cannot be assigned via properties using the 25 #original documented option (because hyphens are not valid for names in 26 #python), e.g cmdline.pre-training = 3 will not work 27 #In these cases the shortened option name should be used 28 #cmdline.pre = 3 29 _Switch(["-clustalw", "clustalw"], ["input"], 30 "Use CLUSTALW output format instead of MFA"), 31 _Option(["-c", "c", "--consistency", "consistency" ], ["input"], 32 lambda x: x in range(0,6), 33 0, 34 "Use 0 <= REPS <= 5 (default: 2) passes of consistency transformation", 35 0), 36 _Option(["-ir", "--iterative-refinement", "iterative-refinement", "ir"], ["input"], 37 lambda x: x in range(0,1001), 38 0, 39 "Use 0 <= REPS <= 1000 (default: 100) passes of iterative-refinement", 40 0), 41 _Option(["-pre", "--pre-training", "pre-training", "pre"], ["input"], 42 lambda x: x in range(0,21), 43 0, 44 "Use 0 <= REPS <= 20 (default: 0) rounds of pretraining", 45 0), 46 _Switch(["-pairs", "pairs"], ["input"], 47 "Generate all-pairs pairwise alignments"), 48 _Switch(["-viterbi", "viterbi"], ["input"], 49 "Use Viterbi algorithm to generate all pairs (automatically enables -pairs)"), 50 _Switch(["-verbose", "verbose"], ["input"], 51 "Report progress while aligning (default: off)"), 52 _Option(["-annot", "annot"], ["input"], 53 None, 54 0, 55 "Write annotation for multiple alignment to FILENAME", 56 0), 57 _Option(["-t", "t", "--train", "train"], ["input"], 58 None, 59 0, 60 "Compute EM transition probabilities, store in FILENAME (default: no training)", 61 0), 62 _Switch(["-e", "e", "--emissions", "emissions"], ["input"], 63 "Also reestimate emission probabilities (default: off)"), 64 _Option(["-p", "p", "--paramfile", "paramfile"], ["input"], 65 None, 66 0, 67 "Read parameters from FILENAME", 68 0), 69 _Switch(["-a", "--alignment-order", "alignment-order", "a"], ["input"], 70 "Print sequences in alignment order rather than input order (default: off)"), 71 #Input file name 72 _Argument(["input"], ["input", "file"], None, 1, 73 "Input file name. Must be multiple FASTA alignment "+ \ 74 "(MFA) format"), 75 ] 76 AbstractCommandline.__init__(self, cmd, **kwargs)
77