Delete unneeded directory

[jabaws.git] / website / archive / binaries / mac / src / globplot / biopython-1.50 / Bio / Fasta / FastaAlign.py

diff --git a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/Fasta/FastaAlign.py b/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/Fasta/FastaAlign.py
deleted file mode 100644 (file)
index 735b502..0000000
--- a/website/archive/binaries/mac/src/globplot/biopython-1.50/Bio/Fasta/FastaAlign.py
+++ /dev/null
@@ -1,84 +0,0 @@
-"""
-Code to deal with alignments written in Fasta format (OBSOLETE).
-
-This module is considered obsolete and likely to be deprecated.  Please use
-Bio.AlignIO instead for reading and writing alignments in FASTA format.
-
-This mostly just uses the regular Fasta parsing stuff written by Jeff
-to deal with all of the input and output formats.
-
-functions:
-o parse_file()
-
-classes:
-FastaAlignment"""
-# standard library
-import os
-
-# biopython
-from Bio.Align.Generic import Alignment
-from Bio import Alphabet
-from Bio.Alphabet import IUPAC
-from Bio import Fasta
-
-def parse_file(file_name, type = 'DNA'):
-    """Parse the given file into a FastaAlignment object.
-
-    Arguments:
-    o file_name - The location of the file to parse.
-    o type - The type of information contained in the file.
-    """
-    if type.upper() == 'DNA':
-        alphabet = IUPAC.ambiguous_dna
-    elif type.upper() == 'RNA':
-        alphabet = IUPAC.ambiguous_rna
-    elif type.upper() == 'PROTEIN':
-        alphabet = IUPAC.protein
-    else:
-        raise ValueError("Invalid type %s passed. Need DNA, RNA or PROTEIN"
-                         % type)
-
-    # create a new alignment object
-    fasta_align = FastaAlignment(Alphabet.Gapped(alphabet))
-
-    # now parse the file and fill up the alignment object
-    align_file = open(file_name, 'r')
-
-    parser = Fasta.RecordParser()
-    iterator = Fasta.Iterator(align_file, parser)
-
-    cur_align = iterator.next()
-    while cur_align:
-        fasta_align.add_sequence(cur_align.title, cur_align.sequence)
-
-        cur_align = iterator.next()
-
-    return fasta_align
-
-class FastaAlignment(Alignment):
-    """Work with the Fasta Alignment format.
-
-    The fasta alignment format is basically the same as the regular ol'
-    Fasta format we know and love, except the sequences have gaps
-    (represented by -'s).
-    """
-    def __init__(self, alphabet = Alphabet.Gapped(IUPAC.ambiguous_dna)):
-        Alignment.__init__(self, alphabet)
-
-    def __str__(self):
-        """Print out a fasta version of the alignment info."""
-        return_string = ''
-        for item in self._records:
-            new_f_record = Fasta.Record()
-            new_f_record.title = item.description
-            new_f_record.sequence = item.seq.data
-
-            return_string = return_string + str(new_f_record) + os.linesep + os.linesep
-
-        # have a extra newline, so strip two off and add one before returning
-        return return_string.rstrip() + os.linesep
-
-            
-            
-        
-