+++ /dev/null
-# Copyright 2008 by Peter Cock. All rights reserved.
-# This code is part of the Biopython distribution and governed by its
-# license. Please see the LICENSE file that should have been included
-# as part of this package.
-
-"""Bio.SeqIO support for the "tab" (simple tab separated) file format.
-
-You are expected to use this module via the Bio.SeqIO functions.
-
-The "tab" format is an ad-hoc plain text file format where each sequence is
-on one (long) line. Each line contains the identifier/description, followed
-by a tab, followed by the sequence. For example, consider the following
-short FASTA format file:
-
->ID123456 possible binding site?
-CATCNAGATGACACTACGACTACGACTCAGACTAC
->ID123457 random sequence
-ACACTACGACTACGACTCAGACTACAAN
-
-Apart from the descriptions, this can be represented in the simple two column
-tab separated format as follows:
-
-ID123456(tab)CATCNAGATGACACTACGACTACGACTCAGACTAC
-ID123457(tab)ACACTACGACTACGACTCAGACTACAAN
-
-When reading this file, "ID123456" or "ID123457" will be taken as the record's
-.id and .name property. There is no other information to record.
-
-Similarly, when writing to this format, Biopython will ONLY record the record's
-.id and .seq (and not the description or any other information) as in the example
-above.
-"""
-
-from Bio.Alphabet import single_letter_alphabet
-from Bio.Seq import Seq
-from Bio.SeqRecord import SeqRecord
-from Interfaces import SequentialSequenceWriter
-
-#This is a generator function!
-def TabIterator(handle, alphabet = single_letter_alphabet) :
- """Iterates over tab separated lines (as SeqRecord objects).
-
- Each line of the file should contain one tab only, dividing the line
- into an identifier and the full sequence.
-
- handle - input file
- alphabet - optional alphabet
-
- The first field is taken as the record's .id and .name (regardless of
- any spaces within the text) and the second field is the sequence.
-
- Any blank lines are ignored.
- """
- for line in handle :
- try :
- title, seq = line.split("\t") #will fail if more than one tab!
- except :
- if line.strip() == "" :
- #It's a blank line, ignore it
- continue
- raise ValueError("Each line should have one tab separating the" + \
- " title and sequence, this line has %i tabs: %s" \
- % (line.count("\t"), repr(line)))
- title = title.strip()
- seq = seq.strip() #removes the trailing new line
- yield SeqRecord(Seq(seq, alphabet), id = title, name = title)
-
-class TabWriter(SequentialSequenceWriter):
- """Class to write simple tab separated format files.
-
- Each line consists of "id(tab)sequence" only.
-
- Any description, name or other annotation is not recorded.
- """
- def write_record(self, record):
- """Write a single tab line to the file."""
- assert self._header_written
- assert not self._footer_written
- self._record_written = True
-
- title = self.clean(record.id)
- seq = self._get_seq_string(record) #Catches sequence being None
- assert "\t" not in title
- assert "\n" not in title
- assert "\r" not in title
- assert "\t" not in seq
- assert "\n" not in seq
- assert "\r" not in seq
- self.handle.write("%s\t%s\n" % (title, seq))
-
-
-if __name__ == "__main__" :
- print "Running quick self test"
- from StringIO import StringIO
-
- #This example has a trailing blank line which should be ignored
- handle = StringIO("Alpha\tAAAAAAA\nBeta\tCCCCCCC\n\n")
- records = list(TabIterator(handle))
- assert len(records) == 2
-
- handle = StringIO("Alpha\tAAAAAAA\tExtra\nBeta\tCCCCCCC\n")
- try :
- records = list(TabIterator(handle))
- assert False, "Should have reject this invalid example!"
- except ValueError :
- #Good!
- pass
-
- print "Done"
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