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1 #!/usr/bin/env python
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2
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3 # Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
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4 #
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5 # This software is distributed under the MIT Open Source License.
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6 # <http://www.opensource.org/licenses/mit-license.html>
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7 #
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8 # Permission is hereby granted, free of charge, to any person obtaining a
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9 # copy of this software and associated documentation files (the "Software"),
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10 # to deal in the Software without restriction, including without limitation
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11 # the rights to use, copy, modify, merge, publish, distribute, sublicense,
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12 # and/or sell copies of the Software, and to permit persons to whom the
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13 # Software is furnished to do so, subject to the following conditions:
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14 #
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15 # The above copyright notice and this permission notice shall be included
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16 # in all copies or substantial portions of the Software.
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17 #
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18 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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19 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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20 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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21 # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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22 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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23 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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24 # THE SOFTWARE.
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25 #
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26
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27 """Read and write a rectangular array of sequence data.
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28
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29 One sequence per line and nothing else. Each line must contain the same number
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30 of characters. Blank lines and white space are ignored.
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31
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32 --- Example Array ---
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33
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34 --------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF
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35 --------------------------LENLEDLF-WELDRLD------NYNDTSLVENH-
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36 --------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY
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37 -----------------------------------YTSDN---------YSGSGDYDSNK
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38 -SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD
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39 --LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD
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40 -SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD
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41 -EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD
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42 """
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43
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44 from corebio.seq import *
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45 from corebio.utils import *
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46
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47 example = """
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48 --------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF
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49 --------------------------LENLEDLF-WELDRLD------NYNDTSLVENH-
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50 --------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY
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51 -----------------------------------YTSDN---------YSGSGDYDSNK
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52 -SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD
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53 --LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD
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54 -SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD
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55 -EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD
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56 """
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57
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58 names = ("array",'flatfile')
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59 extensions = ()
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60
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61 def read(fin, alphabet=None):
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62 """Read a file of raw sequecne alignment data.
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63
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64 Args:
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65 fin -- A stream or file to read
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66 alphabet -- The expected alphabet of the data, if given
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67 Returns:
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68 SeqList -- A list of sequences
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69 Raises:
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70 ValueError -- If the file is unparsable
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71 """
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72 seqs = [ s for s in iterseq(fin, alphabet)]
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73 return SeqList(seqs)
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74
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75
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76 def iterseq(fin, alphabet=None) :
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77 """ Read one line of sequence data and yeild the sequence.
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78
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79 Args:
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80 fin -- A stream or file to read
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81 alphabet -- The expected alphabet of the data, if given
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82 Yeilds:
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83 Seq -- One alphabetic sequence at a time.
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84 Raises:
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85 ValueError -- If the file is unparsable
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86 """
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87
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88 alphabet = Alphabet(alphabet)
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89 line_length = 0
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90
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91 for linenum, line in enumerate(fin) :
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92 if line.isspace(): continue # Blank line
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93 line = line.strip()
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94
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95 if line[0] == '>' : # probable a fasta file. Fail.
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96 raise ValueError(
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97 "Parse Error on input line: %d " % (linenum) )
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98
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99 line = remove_whitespace(line)
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100
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101 if not alphabet.alphabetic(line) :
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102 raise ValueError(
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103 "Character on line: %d not in alphabet: %s : %s" % \
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104 (linenum, alphabet, line) )
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105
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106 if line_length and line_length != len(line) :
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107 raise ValueError("Line %d has a incommensurate length." % linenum)
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108 line_length = len(line)
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109
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110 yield Seq(line, alphabet)
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111
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112
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113 def write(afile, seqs):
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114 """Write raw sequence data, one line per sequence.
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115
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116 arguments:
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117 afile -- A writable stream.
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118 seqs -- A list of Seq's
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119 """
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120 for s in seqs :
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121 writeseq(afile, s)
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122
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123
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124 def writeseq(afile, seq):
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125 """ Write a single sequence in raw format.
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126
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127 arguments:
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128 afile -- A writable stream.
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129 seq -- A Seq instance
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130 """
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131 print >>afile, seq
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132
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133 |
