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2 # Copyright (c) 2006, The Regents of the University of California, through
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3 # Lawrence Berkeley National Laboratory (subject to receipt of any required
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4 # approvals from the U.S. Dept. of Energy). All rights reserved.
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5
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6 # This software is distributed under the new BSD Open Source License.
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7 # <http://www.opensource.org/licenses/bsd-license.html>
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8 #
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9 # Redistribution and use in source and binary forms, with or without
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10 # modification, are permitted provided that the following conditions are met:
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11 #
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12 # (1) Redistributions of source code must retain the above copyright notice,
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13 # this list of conditions and the following disclaimer.
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14 #
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15 # (2) Redistributions in binary form must reproduce the above copyright
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16 # notice, this list of conditions and the following disclaimer in the
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17 # documentation and or other materials provided with the distribution.
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18 #
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19 # (3) Neither the name of the University of California, Lawrence Berkeley
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20 # National Laboratory, U.S. Dept. of Energy nor the names of its contributors
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21 # may be used to endorse or promote products derived from this software
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22 # without specific prior written permission.
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23 #
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24 # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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25 # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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26 # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
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27 # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
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28 # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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29 # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
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30 # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
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31 # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
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32 # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
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33 # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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34 # POSSIBILITY OF SUCH DAMAGE.
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35
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36 """Sequence IO for NBRF/PIR format.
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37
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38 The format is similar to fasta. The header line consistins of '>', a two-
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39 letter sequence type (P1, F1, DL, DC, RL, RC, or XX), a semicolon, and a
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40 sequence ID. The next line is a textual description of the sequence,
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41 followed by one or more lines containing the sequence data. The end of
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42 the sequence is marked by a "*" (asterisk) character.
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43
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44 type_code -- A map between NBRF two letter type codes and Alphabets.
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45
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46
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47 see: http://www.cmbi.kun.nl/bioinf/tools/crab_pir.html
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48
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49 --- Example NBRF File ---
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50
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51 >P1;CRAB_ANAPL
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52 ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
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53 MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR
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54 SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH
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55 GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ
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56 SDVPERSIPI TREEKPAIAG AQRK*
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57
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58 >P1;CRAB_BOVIN
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59 ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN).
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60 MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPA STSLSPFYLR
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61 PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV
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62 HGKHEERQDE HGFISREFHR KYRIPADVDP LAITSSLSSD GVLTVNGPRK
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63 QASGPERTIP ITREEKPAVT AAPKK*
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64
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65 """
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66
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67 from corebio.utils import *
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68 from corebio.seq import *
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69 from corebio.seq_io import *
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70
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71 names = ("nbrf", "pir",)
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72 extensions = ('nbrf', 'pir', 'ali')
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73
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74
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75
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76
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77 type_code = {
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78 'P1' : protein_alphabet, # Protein (complete)
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79 'F1' : protein_alphabet, # Protein (fragment)
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80 'DL' : dna_alphabet, # DNA (linear)
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81 'DC' : dna_alphabet, # DNA (circular)
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82 'RC' : rna_alphabet, # RNA (linear)
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83 'RL' : rna_alphabet, # RNA (circular)
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84 'N3' : rna_alphabet, # tRNA
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85 'N1' : rna_alphabet, # other functional RNA
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86 'XX' : generic_alphabet
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87 }
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88
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89 def read(fin, alphabet=None):
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90 """Read and parse a NBRF seqquence file.
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91
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92 Args:
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93 fin -- A stream or file to read
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94 alphabet -- The expected alphabet of the data. If not supplied, then
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95 an appropriate alphabet will be inferred from the data.
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96 Returns:
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97 SeqList -- A list of sequences
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98 Raises:
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99 ValueError -- If the file is unparsable
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100 """
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101 seqs = [ s for s in iterseq(fin, alphabet)]
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102 return SeqList(seqs)
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103
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104
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105
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106 def iterseq(fin, alphabet=None):
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107 """ Generate sequences from an NBRF file.
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108
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109 arguments:
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110 fin -- A stream or file to read
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111 alphabet --
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112 yeilds :
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113 Seq
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114 raises :
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115 ValueError -- On a parse error.
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116 """
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117
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118 body, header,sequence = range(3) # Internal states
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119
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120 state = body
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121 seq_id = None
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122 seq_desc = None
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123 seq_alpha = None
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124 seqs = []
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125
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126 for lineno, line in enumerate(fin) :
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127 if state == body :
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128 if line == "" or line.isspace() :
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129 continue
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130 if line[0] == '>':
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131 seq_type, seq_id = line[1:].split(';')
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132 if alphabet :
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133 seq_alpha = alphabet
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134 else :
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135 seq_alpha = type_code[seq_type]
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136 state = header
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137 continue
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138 raise ValueError("Parse error on line: %d" % lineno)
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139
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140 elif state == header :
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141 seq_desc = line.strip()
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142 state = sequence
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143 continue
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144
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145 elif state == sequence :
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146 data = "".join(line.split()) # Strip out white space
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147 if data[-1] =='*' :
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148 # End of sequence data
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149 seqs.append(data[:-1])
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150
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151 seq = Seq( "".join(seqs), name = seq_id.strip(),
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152 description = seq_desc, alphabet = seq_alpha)
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153
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154 yield seq
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155 state= body
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156 seq_id = None
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157 seq_desc = None
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158 seqs = []
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159 continue
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160 else :
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161 seqs.append(data)
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162 continue
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163 else :
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164 # If we ever get here something has gone terrible wrong
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165 assert(False)
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166
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167 # end for
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168
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169
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