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1 #!/usr/bin/env python
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2
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3 # Copyright (c) 2005 Clare Gollnick <cgollnick@berkeley.edu>
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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
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28 """Read sequence information in MSF format.
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29
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30 This is a file format for biological sequence data. The sequences are interweaved and each line is labeled with the sequence name. The MSF format can be identified in one, or more of the following ways:
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31 1. The word PileUp on the first line (optional)
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32 2. the word !!AA_MULTIPLE_ALIGNMENT or !!NA_MULTIPLE_ALIGNMENT at the start of the file (optional)
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33 3. the word MSF on the first line of the file, and the characters ".." at the end of this line (optional)
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34 4. A header containing sequence information followed by a line with the characters "//"
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35 """
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36 example= """
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37
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38 PileUp
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39
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40
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41 MSF: 64 Type: P Check: 767 ..
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42
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43 Name: Cow Len: 100 Check: 3761 Weight: 1.00
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44 Name: Carp Len: 100 Check: 1550 Weight: 1.00
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45 Name: Chicken Len: 100 Check: 2397 Weight: 1.00
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46 Name: Human Len: 100 Check: 9021 Weight: 1.00
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47 Name: Loach Len: 100 Check: 984 Weight: 1.00
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48 Name: Mouse Len: 100 Check: 2993 Weight: 1.00
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49
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50
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51 //
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52
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53
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54 Cow MAYPMQLGFQ DATSPIMEEL LHFHDHTLMI VFLISSLVLY IISLMLTTKL
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55 Carp MAHPTQLGFK DAAMPVMEEL LHFHDHALMI VLLISTLVLY IITAMVSTKL
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56 Chicken MANHSQLGFQ DASSPIMEEL VEFHDHALMV ALAICSLVLY LLTLMLMEKL
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57 Human MAHAAQVGLQ DATSPIMEEL ITFHDHALMI IFLICFLVLY ALFLTLTTKL
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58 Loach MAHPTQLGFQ DAASPVMEEL LHFHDHALMI VFLISALVLY VIITTVSTKL
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59 Mouse MAYPFQLGLQ DATSPIMEEL MNFHDHTLMI VFLISSLVLY IISLMLTTKL
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60
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61
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62
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63 Cow THTSTMDAQE VETIWTILPA IILILIALPS LRILYMMDEI NNPSLTVKTM
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64 Carp TNKYILDSQE IEIVWTILPA VILVLIALPS LRILYLMDEI NDPHLTIKAM
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65 Chicken S.SNTVDAQE VELIWTILPA IVLVLLALPS LQILYMMDEI DEPDLTLKAI
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66 Human TNTNISDAQE METVWTILPA IILVLIALPS LRILYMTDEV NDPSLTIKSI
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67 Loach TNMYILDSQE IEIVWTVLPA LILILIALPS LRILYLMDEI NDPHLTIKAM
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68 Mouse THTSTMDAQE VETIWTILPA VILIMIALPS LRILYMMDEI NNPVLTVKTM
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69
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70 """
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71
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72 import re
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73
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74 from corebio.seq import *
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75 from corebio.seq_io import *
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76 from corebio.utils import *
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77
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78 names = ('msf', 'gcg-msf', 'gcg', 'PileUp')
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79 extensions = ('msf')
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80
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81 end_header=re.compile(r'(//)(\s*)$')
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82 seq_line=re.compile(r'\s*(\S+)\s+([\S\s.?]+)$')
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83
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84 def iterseq(fin, alphabet=None):
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85 """Iterate over the sequences in the file."""
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86 # Default implementation
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87 return iter(read(fin, alphabet) )
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88
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89
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90
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91 def read(fin, alphabet=None):
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92 alphabet =Alphabet(alphabet)
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93 seq_ids=[]
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94 seqs=[]
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95 block_count=0
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96
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97 for token in _line_is(fin):
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98 if token.typeof=="begin_block":
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99 block_count=0
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100
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101 elif token.typeof == "seq_id":
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102 if len(seqs)<= block_count:
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103 seq_ids.append(token.data)
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104 seqs.append([])
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105 elif token.typeof=="seq":
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106 if not alphabet.alphabetic(token.data):
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107 raise ValueError(
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108 "Character on line: %d not in alphabet: %s : %s" % (
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109 token.lineno, alphabet, token.data) )
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110 seqs[block_count].append(token.data)
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111 block_count +=1
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112 if seq_ids==[]:
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113 raise ValueError("Parse error, possible wrong format")
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114 seqs = [ Seq("".join(s), alphabet, name= i) for s,i in zip(seqs,seq_ids)]
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115 return SeqList(seqs)
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116
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117 def _line_is(fin):
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118 header, body, block = range(3)
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119 yield Token("begin")
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120 state=header
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121 for L, line in enumerate(fin):
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122 if state==header:
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123 if line.isspace():continue
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124 m=end_header.match(line)
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125 if m is not None:
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126 yield Token("end_header")
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127 state=body
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128 continue
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129 else: continue
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130
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131 if state==body:
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132 if line.isspace():continue
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133 yield Token("begin_block")
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134 state=block
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135 #skips to a block of sequences
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136
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137 if state==block:
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138 if line.isspace():
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139 yield Token("end_block")
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140 state=body
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141 continue
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142 m=seq_line.match(line)
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143 if m is None:
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144 raise ValueError("Parse error on line: %d" % L)
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145 if m.group(1).isdigit() and m.group(2).strip().isdigit():
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146 continue
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147 yield Token("seq_id",m.group(1).strip() )
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148 data=m.group(2)
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149 data="".join((data.split()))
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150 yield Token("seq",data.strip() )
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151
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152
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153
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154
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155
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156 |
