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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 sequence information in IntelliGenetics format.
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28
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29 A sequence file in IG format can contain several sequences, each consisting of a
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30 number of comment lines that must begin with a semicolon (";"), a line with the
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31 sequence name and the sequence itself terminated with the termination character
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32 '1' for linear or '2' for circular sequences. The termination caracter is
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33 defacto optional.
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34
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35 --- Example IG File ---
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36
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37 ;H.sapiens fau mRNA, 518 bases
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38 HSFAU
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39 ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc
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40 actcttaagtcttttgtaattctggctttctctaataaaaaagccactta
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41 gttcagtcaaaaaaaaaa1
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42 ;H.sapiens fau 1 gene, 2016 bases
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43 HSFAU1
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44 ctaccattttccctctcgattctatatgtacactcgggacaagttctcct
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45 gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg
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46 gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc
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47 tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac
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48 accggttctccatccccgcagcgtagcccggaacatggtagctgccatct
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49 ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgcccc2
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50
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51 """
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52
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53 from corebio.utils import *
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54 from corebio.seq import *
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55 from corebio.seq_io import *
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56
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57
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58 names = ( 'intelligenetics', 'ig', 'stanford', )
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59 extensions = ('ig')
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60
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61
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62 example = """
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63 ;H.sapiens fau mRNA, 518 bases
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64 HSFAU
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65 ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc
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66 actcttaagtcttttgtaattctggctttctctaataaaaaagccactta
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67 gttcagtcaaaaaaaaaa1
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68 ;H.sapiens fau 1 gene, 2016 bases
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69 HSFAU1
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70 ctaccattttccctctcgattctatatgtacactcgggacaagttctcct
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71 gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg
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72 gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc
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73 tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac
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74 accggttctccatccccgcagcgtagcccggaacatggtagctgccatct
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75 ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgcccc2
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76 """
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77
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78
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79
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80
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81 def read(fin, alphabet=None):
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82 """Read and parse an IG file.
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83
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84 Args:
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85 fin -- A stream or file to read
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86 alphabet -- The expected alphabet of the data, if given
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87 Returns:
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88 SeqList -- A list of sequences
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89 Raises:
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90 ValueError -- If the file is unparsable
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91 """
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92 seqs = [ s for s in iterseq(fin, alphabet)]
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93 return SeqList(seqs)
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94
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95
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96 def iterseq(fin, alphabet=None):
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97 """ Parse an IG file and generate sequences.
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98
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99 Args:
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100 fin -- A stream or file to read
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101 alphabet -- The expected alphabet of the data, if given
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102 Yeilds:
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103 Seq -- One alphabetic sequence at a time.
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104 Raises:
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105 ValueError -- If the file is unparsable
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106 """
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107 alphabet = Alphabet(alphabet)
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108
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109 seqs = []
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110 header = []
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111 start_lineno = -1
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112 name = None
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113
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114 def build_seq(seqs,alphabet, name, comments, lineno) :
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115 try :
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116 desc = '\n'.join(comments)
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117 s = Seq( "".join(seqs), alphabet, name=name, description=desc)
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118 except ValueError :
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119 raise ValueError(
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120 "Parsed failed with sequence starting at line %d: "
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121 "Character not in alphabet: %s" % (lineno, alphabet) )
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122 return s
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123
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124 for lineno, line in enumerate(fin) :
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125 line = line.strip()
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126 if line == '' : continue
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127 if line.startswith(';') :
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128 if seqs :
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129 # end of sequence
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130 yield build_seq(seqs,alphabet, name, header, start_lineno)
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131 header = []
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132 seqs = []
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133 name = None
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134 header.append(line[1:])
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135 start_lineno = lineno
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136 elif not name :
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137 name = line
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138 elif line[-1] == '1' or line[-1]=='2':
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139 # End of sequence
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140 seqs.append(remove_whitespace(line[0:-1]))
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141 yield build_seq(seqs,alphabet, name, header, start_lineno)
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142 header = []
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143 seqs = []
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144 name = None
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145 else:
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146 seqs.append( remove_whitespace(line))
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147
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148 if seqs :
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149 yield build_seq(seqs,alphabet, name, header, start_lineno)
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150 return
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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 def write(fout, seqs):
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157 """Write an IG file.
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158
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159 Args:
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160 fout -- A writable stream.
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161 seqs -- A list of Seq's
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162 Raises:
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163 ValueError -- If a sequence is missing a name
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164 """
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165 for s in seqs :
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166 writeseq(fout, s)
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167
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168
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169 def writeseq(fout, seq):
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170 """ Write a single sequence in IG format.
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171
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172 Args:
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173 afile -- A writable stream.
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174 seq -- A Seq instance
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175 Raises:
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176 ValueError -- If a sequence is missing a name
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177 """
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178
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179 desc = seq.description or ''
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180
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181 # We prepend ';' to each line
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182 for h in desc.splitlines() :
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183 print >> fout, ';' +h
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184
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185 if not seq.name :
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186 raise ValueError(
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187 "Write failed with missing sequence name: %s"% str(seq) )
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188 print >>fout, seq.name
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189 L = len(seq)
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190 line_length = 80
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191 for n in range (1+ int(L/line_length)) :
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192 print >>fout, seq[n * line_length: (n+1) * line_length]
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193 print >>fout
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