1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
|
#!/usr/bin/env python
# Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# the rights to use, copy, modify, merge, publish, distribute, sublicense,
# and/or sell copies of the Software, and to permit persons to whom the
# Software is furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included
# in all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
"""Read and write sequence information in IntelliGenetics format.
A sequence file in IG format can contain several sequences, each consisting of a
number of comment lines that must begin with a semicolon (";"), a line with the
sequence name and the sequence itself terminated with the termination character
'1' for linear or '2' for circular sequences. The termination character is
defacto optional.
--- Example IG File ---
;H.sapiens fau mRNA, 518 bases
HSFAU
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc
actcttaagtcttttgtaattctggctttctctaataaaaaagccactta
gttcagtcaaaaaaaaaa1
;H.sapiens fau 1 gene, 2016 bases
HSFAU1
ctaccattttccctctcgattctatatgtacactcgggacaagttctcct
gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg
gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc
tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac
accggttctccatccccgcagcgtagcccggaacatggtagctgccatct
ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgcccc2
"""
from typing import Iterator, List, Optional, TextIO
from ..seq import Alphabet, Seq, SeqList
from ..utils import remove_whitespace
names = (
"intelligenetics",
"ig",
"stanford",
)
extensions = ("ig",)
example = """
;H.sapiens fau mRNA, 518 bases
HSFAU
ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc
actcttaagtcttttgtaattctggctttctctaataaaaaagccactta
gttcagtcaaaaaaaaaa1
;H.sapiens fau 1 gene, 2016 bases
HSFAU1
ctaccattttccctctcgattctatatgtacactcgggacaagttctcct
gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg
gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc
tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac
accggttctccatccccgcagcgtagcccggaacatggtagctgccatct
ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgcccc2
"""
def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList:
"""Read and parse an IG file.
Args:
fin -- A stream or file to read
alphabet -- The expected alphabet of the data, if given
Returns:
SeqList -- A list of sequences
Raises:
ValueError -- If the file is unparsable
"""
seqs = [s for s in iterseq(fin, alphabet)]
return SeqList(seqs)
def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]:
"""Parse an IG file and generate sequences.
Args:
fin -- A stream or file to read
alphabet -- The expected alphabet of the data, if given
Yields:
Seq -- One alphabetic sequence at a time.
Raises:
ValueError -- If the file is unparsable
"""
alphabet = Alphabet(alphabet)
seqs: list = []
header: list = []
start_lineno = -1
name = None
def build_seq(
seqs: List[str],
alphabet: Alphabet,
name: Optional[str],
comments: List[str],
lineno: int,
) -> Seq:
try:
desc = "\n".join(comments)
s = Seq("".join(seqs), alphabet, name=name, description=desc)
except ValueError:
raise ValueError(
"Parse failed with sequence starting at line %d: "
"Character not in alphabet: %s" % (lineno, alphabet)
)
return s
for lineno, line in enumerate(fin):
line = line.strip()
if line == "":
continue
if line.startswith(";"):
if seqs:
# end of sequence
yield build_seq(seqs, alphabet, name, header, start_lineno)
header = []
seqs = []
name = None
header.append(line[1:])
start_lineno = lineno
elif not name:
name = line
elif line[-1] == "1" or line[-1] == "2":
# End of sequence
seqs.append(remove_whitespace(line[0:-1]))
yield build_seq(seqs, alphabet, name, header, start_lineno)
header = []
seqs = []
name = None
else:
seqs.append(remove_whitespace(line))
if seqs:
yield build_seq(seqs, alphabet, name, header, start_lineno)
return
def write(fout: TextIO, seqs: SeqList) -> None:
"""Write an IG file.
Args:
fout -- A writable stream.
seqs -- A list of Seq's
Raises:
ValueError -- If a sequence is missing a name
"""
for s in seqs:
writeseq(fout, s)
def writeseq(fout: TextIO, seq: Seq) -> None:
"""Write a single sequence in IG format.
Args:
fout -- A writable stream.
seq -- A Seq instance
Raises:
ValueError -- If a sequence is missing a name
"""
desc = seq.description or ""
# We prepend ';' to each line
for h in desc.splitlines():
print(";" + h, file=fout)
if not seq.name:
raise ValueError("Write failed with missing sequence name: %s" % str(seq))
print(seq.name, file=fout)
L = len(seq)
line_length = 80
for n in range(1 + L // line_length):
print(seq[n * line_length : (n + 1) * line_length], file=fout)
print(file=fout)
|
