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

  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   
  6  """ 
  7  Bio.Application command line for the multiple alignment program DIALIGN2-2. 
  8   
  9  http://bibiserv.techfak.uni-bielefeld.de/dialign/welcome.html 
 10   
 11  Citations: 
 12   
 13  B. Morgenstern (2004). DIALIGN: Multiple DNA and Protein Sequence Alignment 
 14  at BiBiServ. Nucleic Acids Research 32, W33-W36. 
 15   
 16  Last checked against version: 2.2 
 17  """ 
 18   
 19  from Bio import Application 
 20  from Bio.Application import _Option, _Argument, _Switch, AbstractCommandline 
 21   
22 -class DialignCommandline(AbstractCommandline):
23 """Command line wrapper for the multiple alignment program DIALIGN2-2."""
24 - def __init__(self, cmd="dialign2-2", **kwargs):
25 self.program_name = cmd 26 self.parameters = \ 27 [ 28 _Switch(["-afc", "afc"], ["input"], 29 "Creates additional output file '*.afc' " + \ 30 "containing data of all fragments considered " + \ 31 "for alignment WARNING: this file can be HUGE !"), 32 _Switch(["-afc_v", "afc_v"], ["input"], 33 "Like '-afc' but verbose: fragments are explicitly " + \ 34 "printed. WARNING: this file can be EVEN BIGGER !"), 35 _Switch(["-anc", "anc"], ["input"], 36 "Anchored alignment. Requires a file <seq_file>.anc " + \ 37 "containing anchor points."), 38 _Switch(["-cs", "cs"], ["input"], 39 "If segments are translated, not only the `Watson " + \ 40 "strand' but also the `Crick strand' is looked at."), 41 _Switch(["-cw", "cw"], ["input"], 42 "Additional output file in CLUSTAL W format."), 43 _Switch(["-ds", "ds"], ["input"], 44 "`dna alignment speed up' - non-translated nucleic acid " + \ 45 "fragments are taken into account only if they start " + \ 46 "with at least two matches. Speeds up DNA alignment at " + \ 47 "the expense of sensitivity."), 48 _Switch(["-fa", "fa"], ["input"], 49 "Additional output file in FASTA format."), 50 _Switch(["-ff", "ff"], ["input"], 51 "Creates file *.frg containing information about all " + \ 52 "fragments that are part of the respective optimal " + \ 53 "pairwise alignmnets plus information about " + \ 54 "consistency in the multiple alignment"), 55 _Option(["-fn", "fn"], ["input"], 56 None, 57 0, 58 "Output files are named <out_file>.<extension>.", 59 0), 60 _Switch(["-fop", "fop"], ["input"], 61 "Creates file *.fop containing coordinates of all " + \ 62 "fragments that are part of the respective pairwise alignments."), 63 _Switch(["-fsm", "fsm"], ["input"], 64 "Creates file *.fsm containing coordinates of all " + \ 65 "fragments that are part of the final alignment"), 66 _Switch(["-iw", "iw"], ["input"], 67 "Overlap weights switched off (by default, overlap " + \ 68 "weights are used if up to 35 sequences are aligned). " + \ 69 "This option speeds up the alignment but may lead " + \ 70 "to reduced alignment quality."), 71 _Switch(["-lgs", "lgs"], ["input"], 72 "`long genomic sequences' - combines the following " + \ 73 "options: -ma, -thr 2, -lmax 30, -smin 8, -nta, -ff, " + \ 74 "-fop, -ff, -cs, -ds, -pst "), 75 _Switch(["-lgs_t", "lgs_t"], ["input"], 76 "Like '-lgs' but with all segment pairs assessed " + \ 77 "at the peptide level (rather than 'mixed alignments' " + \ 78 "as with the '-lgs' option). Therefore faster than " + \ 79 "-lgs but not very sensitive for non-coding regions."), 80 _Option(["-lmax", "lmax"], ["input"], 81 lambda x: isinstance(x, int), 82 0, 83 "Maximum fragment length = x (default: x = 40 or " + \ 84 "x = 120 for `translated' fragments). Shorter x " + \ 85 "speeds up the program but may affect alignment quality.", 86 0), 87 _Switch(["-lo", "lo"], ["input"], 88 "(Long Output) Additional file *.log with information " + \ 89 "about fragments selected for pairwise alignment and " + \ 90 "about consistency in multi-alignment proceedure."), 91 _Switch(["-ma", "ma"], ["input"], 92 "`mixed alignments' consisting of P-fragments and " + \ 93 "N-fragments if nucleic acid sequences are aligned."), 94 _Switch(["-mask", "mask"], ["input"], 95 "Residues not belonging to selected fragments are " + \ 96 "replaced by `*' characters in output alignment " + \ 97 "(rather than being printed in lower-case characters)"), 98 _Switch(["-mat", "mat"], ["input"], 99 "Creates file *mat with substitution counts derived " + \ 100 "from the fragments that have been selected for alignment."), 101 _Switch(["-mat_thr", "mat_thr"], ["input"], 102 "Like '-mat' but only fragments with weight score " + \ 103 "> t are considered"), 104 _Switch(["-max_link", "max_link"], ["input"], 105 "'maximum linkage' clustering used to construct " + \ 106 "sequence tree (instead of UPGMA)."), 107 _Switch(["-min_link", "min_link"], ["input"], 108 "'minimum linkage' clustering used."), 109 _Option(["-mot", "mot"], ["input"], 110 None, 111 0, 112 "'motif' option.", 113 0), 114 _Switch(["-msf", "msf"], ["input"], 115 "Separate output file in MSF format."), 116 _Switch(["-n", "n"], ["input"], 117 "Input sequences are nucleic acid sequences. " + \ 118 "No translation of fragments."), 119 _Switch(["-nt", "nt"], ["input"], 120 "Input sequences are nucleic acid sequences and " + \ 121 "`nucleic acid segments' are translated to `peptide " + \ 122 "segments'."), 123 _Switch(["-nta", "nta"], ["input"], 124 "`no textual alignment' - textual alignment suppressed. " + \ 125 "This option makes sense if other output files are of " + \ 126 "intrest -- e.g. the fragment files created with -ff, " + \ 127 "-fop, -fsm or -lo."), 128 _Switch(["-o", "o"], ["input"], 129 "Fast version, resulting alignments may be slightly " + \ 130 "different."), 131 _Switch(["-ow", "ow"], ["input"], 132 "Overlap weights enforced (By default, overlap weights " + \ 133 "are used only if up to 35 sequences are aligned since " + \ 134 "calculating overlap weights is time consuming)."), 135 _Switch(["-pst", "pst"], ["input"], 136 "'print status'. Creates and updates a file *.sta with " + \ 137 "information about the current status of the program " + \ 138 "run. This option is recommended if large data sets " + \ 139 "are aligned since it allows the user to estimate the " + \ 140 "remaining running time."), 141 _Switch(["-smin", "smin"], ["input"], 142 "Minimum similarity value for first residue pair " + \ 143 "(or codon pair) in fragments. Speeds up protein " + \ 144 "alignment or alignment of translated DNA fragments " + \ 145 "at the expense of sensitivity."), 146 _Option(["-stars", "stars"], ["input"], 147 lambda x: x in range(0,10), 148 0, 149 "Maximum number of `*' characters indicating degree " + \ 150 "of local similarity among sequences. By default, no " + \ 151 "stars are used but numbers between 0 and 9, instead.", 152 0), 153 _Switch(["-stdo", "stdo"], ["input"], 154 "Results written to standard output."), 155 _Switch(["-ta", "ta"], ["input"], 156 "Standard textual alignment printed (overrides " + \ 157 "suppression of textual alignments in special " + \ 158 "options, e.g. -lgs)"), 159 _Option(["-thr", "thr"], ["input"], 160 lambda x: isinstance(x, int), 161 0, 162 "Threshold T = x.", 163 0), 164 _Switch(["-xfr", "xfr"], ["input"], 165 "'exclude fragments' - list of fragments can be " + \ 166 "specified that are NOT considered for pairwise alignment"), 167 _Argument(["input"], ["input", "file"], None, 1, 168 "Input file name. Must be FASTA format") 169 ] 170 AbstractCommandline.__init__(self, cmd, **kwargs)
171