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1 #!/usr/bin/env python
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2
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3 # Copyright (c) 2005 David D. Ding <dding@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 """Read Sequences in interleaved Phylip format (not sequential) and returns a
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28 list of sequences. Phylips is a very common phylogeny generating sequence type
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29 that has the following traits
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30 1) First line contains number of species and number of characters in a species'
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31 sequence. Options can may follow, and they can be spaced or unspaced. Options are
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32 simply letters such as A and W after the number of characters.
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33 2) Options doesn't have to contain U in order for a usertree to appear.
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34 3) If there are options then options appear first, then the sequences. For the
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35 first iteration of sequences the first ten spaces are reserved for names of
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36 options and species, the rest is for sequences.
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37 4) For the second and following iterations the names are removed, only
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38 sequence appears
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39 4) At end of file an usertree may appear. First there is a number that indicts
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40 the number of lines the usertree will take, and then the usertrees follow.
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41
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42 Examples:
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43 6 50 W
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44 W 0101001111 0101110101 01011
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45 dmras1 GTCGTCGTTG GACCTGGAGG CGTGG
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46 hschras GTGGTGGTGG GCGCCGGCCG TGTGG
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47 ddrasa GTTATTGTTG GTGGTGGTGG TGTCG
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48 spras GTAGTTGTAG GAGATGGTGG TGTTG
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49 scras1 GTAGTTGTCG GTGGAGGTGG CGTTG
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50 scras2 GTCGTCGTTG GTGGTGGTGG TGTTG
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51
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52 0101001111 0101110101 01011
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53 GTCGTCGTTG GACCTGGAGG CGTGG
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54 GTGGTGGTGG GCGCCGGCCG TGTGG
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55 GTTATTGTTG GTGGTGGTGG TGTCG
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56 GTAGTTGTAG GAGATGGTGG TGTTG
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57 GTAGTTGTCG GTGGAGGTGG CGTTG
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58 GTCGTCGTTG GTGGTGGTGG TGTTG
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59
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60 1
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61 ((dmras1,ddrasa),((hschras,spras),(scras1,scras2)));
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62
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63
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64 """
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65
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66 from corebio.seq import *
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67
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68 names = ( 'phylip',)
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69 extensions = ('phy',)
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70
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71 def iterseq(fin, alphabet=None):
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72 """Iterate over the sequences in the file."""
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73 # Default implementation
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74 return iter(read(fin, alphabet) )
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75
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76
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77 #Read takes in a phylip file name, read it, processes it, and returns a SeqList
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78 def read(fin, alphabet=None):
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79
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80
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81 sequence=[] #where sequences are stored
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82 idents=[]
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83 num_seq=0
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84 num_total_seq=0 #length of sequence of 1 species
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85 tracker=0 #track what sequence the line is on
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86 usertree_tracker=0 #track usertree lines
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87 options='' #options
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88 num_options=0 #number/lens of options - U
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89
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90 line=fin.readline()
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91 while line:
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92 s_line=line.split() #for ease of use, not used in all scenarios, but easier on the eye
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93
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94 if s_line == []: #see nothing do nothing
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95 pass
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96
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97 elif (s_line[0].isdigit() and len(s_line) == 1 and len(sequence)==num_seq and len(sequence[0])==num_total_seq): #identifies usertree
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98 usertree_tracker = int(s_line[0])
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99 pass
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100
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101 elif num_options > 0:
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102 if len(sequence) < num_seq:
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103 if s_line[0][0] in options:
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104 num_options -= 1
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105 pass
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106 else:
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107 raise ValueError('Not an option, but it should be one')
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108 else:
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109 num_options -= 1
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110 pass
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111
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112 elif usertree_tracker > 0: #baskically skip usertree
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113 if len(sequence[num_seq-1]) == num_total_seq:
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114 usertree_tracker -=1
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115 pass
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116 else:
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117 raise ValueError('User Tree in Wrong Place')
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118
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119 #####problems parse error unexpected
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120 elif s_line[0].isdigit():
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121 if len(s_line) >= 2 and len(sequence) == 0: #identifies first line of file
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122 num_seq = int(s_line[0]) #get number of sequences
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123 num_total_seq = int(s_line[1]) #get length of sequences
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124 if len(s_line) > 2: #takes care of the options
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125 options= (''.join(s_line[2:]))
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126 num_options=len(options) - options.count('U')
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127 else:
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128 raise ValueError('parse error')
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129
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130
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131 #when options end, this take care of the sequence
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132 elif num_options == 0:
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133 if (num_seq==0):
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134 raise ValueError("Empty File, or possibly wrong file")
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135 elif tracker < num_seq:
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136 if num_seq > len(sequence):
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137 sequence.append(''.join(line[10:].split())) #removes species name
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138 idents.append(line[0:10].strip())
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139 tracker +=1
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140
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141 else:
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142 sequence[tracker] += (''.join(s_line))
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143 tracker +=1
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144
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145 if tracker == num_seq:
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146 tracker = 0
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147 num_options = len(options)-options.count('U')
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148
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149 line=fin.readline()
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150
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151 if len(sequence) != len(idents) or len(sequence)!=num_seq:
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152 raise ValueError("Number of different sequences wrong")
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153
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154 seqs = []
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155 for i in range (0, len(idents)):
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156 if len(sequence[i])==num_total_seq:
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157 seqs.append(Seq(sequence[i], alphabet, idents[i]))
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158 else:
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159 raise ValueError("extra sequence in list")
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160
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161 return SeqList(seqs)
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162
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163
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164
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165
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166
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