Mac binaries

[jabaws.git] / website / archive / binaries / mac / src / disembl / biopython-1.50 / Bio / SeqIO / TabIO.py

diff --git a/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/SeqIO/TabIO.py b/website/archive/binaries/mac/src/disembl/biopython-1.50/Bio/SeqIO/TabIO.py
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+# 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"