1 # Copyright 2008 by Peter Cock. All rights reserved.
2 # This code is part of the Biopython distribution and governed by its
3 # license. Please see the LICENSE file that should have been included
4 # as part of this package.
6 """Bio.SeqIO support for the "tab" (simple tab separated) file format.
8 You are expected to use this module via the Bio.SeqIO functions.
10 The "tab" format is an ad-hoc plain text file format where each sequence is
11 on one (long) line. Each line contains the identifier/description, followed
12 by a tab, followed by the sequence. For example, consider the following
13 short FASTA format file:
15 >ID123456 possible binding site?
16 CATCNAGATGACACTACGACTACGACTCAGACTAC
17 >ID123457 random sequence
18 ACACTACGACTACGACTCAGACTACAAN
20 Apart from the descriptions, this can be represented in the simple two column
21 tab separated format as follows:
23 ID123456(tab)CATCNAGATGACACTACGACTACGACTCAGACTAC
24 ID123457(tab)ACACTACGACTACGACTCAGACTACAAN
26 When reading this file, "ID123456" or "ID123457" will be taken as the record's
27 .id and .name property. There is no other information to record.
29 Similarly, when writing to this format, Biopython will ONLY record the record's
30 .id and .seq (and not the description or any other information) as in the example
34 from Bio.Alphabet import single_letter_alphabet
35 from Bio.Seq import Seq
36 from Bio.SeqRecord import SeqRecord
37 from Interfaces import SequentialSequenceWriter
39 #This is a generator function!
40 def TabIterator(handle, alphabet = single_letter_alphabet) :
41 """Iterates over tab separated lines (as SeqRecord objects).
43 Each line of the file should contain one tab only, dividing the line
44 into an identifier and the full sequence.
47 alphabet - optional alphabet
49 The first field is taken as the record's .id and .name (regardless of
50 any spaces within the text) and the second field is the sequence.
52 Any blank lines are ignored.
56 title, seq = line.split("\t") #will fail if more than one tab!
58 if line.strip() == "" :
59 #It's a blank line, ignore it
61 raise ValueError("Each line should have one tab separating the" + \
62 " title and sequence, this line has %i tabs: %s" \
63 % (line.count("\t"), repr(line)))
65 seq = seq.strip() #removes the trailing new line
66 yield SeqRecord(Seq(seq, alphabet), id = title, name = title)
68 class TabWriter(SequentialSequenceWriter):
69 """Class to write simple tab separated format files.
71 Each line consists of "id(tab)sequence" only.
73 Any description, name or other annotation is not recorded.
75 def write_record(self, record):
76 """Write a single tab line to the file."""
77 assert self._header_written
78 assert not self._footer_written
79 self._record_written = True
81 title = self.clean(record.id)
82 seq = self._get_seq_string(record) #Catches sequence being None
83 assert "\t" not in title
84 assert "\n" not in title
85 assert "\r" not in title
86 assert "\t" not in seq
87 assert "\n" not in seq
88 assert "\r" not in seq
89 self.handle.write("%s\t%s\n" % (title, seq))
92 if __name__ == "__main__" :
93 print "Running quick self test"
94 from StringIO import StringIO
96 #This example has a trailing blank line which should be ignored
97 handle = StringIO("Alpha\tAAAAAAA\nBeta\tCCCCCCC\n\n")
98 records = list(TabIterator(handle))
99 assert len(records) == 2
101 handle = StringIO("Alpha\tAAAAAAA\tExtra\nBeta\tCCCCCCC\n")
103 records = list(TabIterator(handle))
104 assert False, "Should have reject this invalid example!"