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comparison corebio/seq_io/array_io.py @ 0:c55bdc2fb9fa

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author davidmurphy
date Thu, 27 Oct 2011 12:09:09 -0400
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1 #!/usr/bin/env python
2
3 # Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
4 #
5 # This software is distributed under the MIT Open Source License.
6 # <http://www.opensource.org/licenses/mit-license.html>
7 #
8 # Permission is hereby granted, free of charge, to any person obtaining a
9 # copy of this software and associated documentation files (the "Software"),
10 # to deal in the Software without restriction, including without limitation
11 # the rights to use, copy, modify, merge, publish, distribute, sublicense,
12 # and/or sell copies of the Software, and to permit persons to whom the
13 # Software is furnished to do so, subject to the following conditions:
14 #
15 # The above copyright notice and this permission notice shall be included
16 # in all copies or substantial portions of the Software.
17 #
18 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
19 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
20 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
21 # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
22 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
23 # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
24 # THE SOFTWARE.
25 #
26
27 """Read and write a rectangular array of sequence data.
28
29 One sequence per line and nothing else. Each line must contain the same number
30 of characters. Blank lines and white space are ignored.
31
32 --- Example Array ---
33
34 --------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF
35 --------------------------LENLEDLF-WELDRLD------NYNDTSLVENH-
36 --------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY
37 -----------------------------------YTSDN---------YSGSGDYDSNK
38 -SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD
39 --LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD
40 -SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD
41 -EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD
42 """
43
44 from corebio.seq import *
45 from corebio.utils import *
46
47 example = """
48 --------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF
49 --------------------------LENLEDLF-WELDRLD------NYNDTSLVENH-
50 --------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY
51 -----------------------------------YTSDN---------YSGSGDYDSNK
52 -SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD
53 --LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD
54 -SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD
55 -EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD
56 """
57
58 names = ("array",'flatfile')
59 extensions = ()
60
61 def read(fin, alphabet=None):
62 """Read a file of raw sequecne alignment data.
63
64 Args:
65 fin -- A stream or file to read
66 alphabet -- The expected alphabet of the data, if given
67 Returns:
68 SeqList -- A list of sequences
69 Raises:
70 ValueError -- If the file is unparsable
71 """
72 seqs = [ s for s in iterseq(fin, alphabet)]
73 return SeqList(seqs)
74
75
76 def iterseq(fin, alphabet=None) :
77 """ Read one line of sequence data and yeild the sequence.
78
79 Args:
80 fin -- A stream or file to read
81 alphabet -- The expected alphabet of the data, if given
82 Yeilds:
83 Seq -- One alphabetic sequence at a time.
84 Raises:
85 ValueError -- If the file is unparsable
86 """
87
88 alphabet = Alphabet(alphabet)
89 line_length = 0
90
91 for linenum, line in enumerate(fin) :
92 if line.isspace(): continue # Blank line
93 line = line.strip()
94
95 if line[0] == '>' : # probable a fasta file. Fail.
96 raise ValueError(
97 "Parse Error on input line: %d " % (linenum) )
98
99 line = remove_whitespace(line)
100
101 if not alphabet.alphabetic(line) :
102 raise ValueError(
103 "Character on line: %d not in alphabet: %s : %s" % \
104 (linenum, alphabet, line) )
105
106 if line_length and line_length != len(line) :
107 raise ValueError("Line %d has a incommensurate length." % linenum)
108 line_length = len(line)
109
110 yield Seq(line, alphabet)
111
112
113 def write(afile, seqs):
114 """Write raw sequence data, one line per sequence.
115
116 arguments:
117 afile -- A writable stream.
118 seqs -- A list of Seq's
119 """
120 for s in seqs :
121 writeseq(afile, s)
122
123
124 def writeseq(afile, seq):
125 """ Write a single sequence in raw format.
126
127 arguments:
128 afile -- A writable stream.
129 seq -- A Seq instance
130 """
131 print >>afile, seq
132
133