Package Bio :: Package Fasta :: Module FastaAlign
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Source Code for Module Bio.Fasta.FastaAlign

 1  """ 
 2  Code to deal with alignments written in Fasta format (OBSOLETE). 
 3   
 4  This module is considered obsolete and likely to be deprecated.  Please use 
 5  Bio.AlignIO instead for reading and writing alignments in FASTA format. 
 6   
 7  This mostly just uses the regular Fasta parsing stuff written by Jeff 
 8  to deal with all of the input and output formats. 
 9   
10  functions: 
11  o parse_file() 
12   
13  classes: 
14  FastaAlignment""" 
15  # standard library 
16  import os 
17   
18  # biopython 
19  from Bio.Align.Generic import Alignment 
20  from Bio import Alphabet 
21  from Bio.Alphabet import IUPAC 
22  from Bio import Fasta 
23   
24 -def parse_file(file_name, type = 'DNA'):
25 """Parse the given file into a FastaAlignment object. 26 27 Arguments: 28 o file_name - The location of the file to parse. 29 o type - The type of information contained in the file. 30 """ 31 if type.upper() == 'DNA': 32 alphabet = IUPAC.ambiguous_dna 33 elif type.upper() == 'RNA': 34 alphabet = IUPAC.ambiguous_rna 35 elif type.upper() == 'PROTEIN': 36 alphabet = IUPAC.protein 37 else: 38 raise ValueError("Invalid type %s passed. Need DNA, RNA or PROTEIN" 39 % type) 40 41 # create a new alignment object 42 fasta_align = FastaAlignment(Alphabet.Gapped(alphabet)) 43 44 # now parse the file and fill up the alignment object 45 align_file = open(file_name, 'r') 46 47 parser = Fasta.RecordParser() 48 iterator = Fasta.Iterator(align_file, parser) 49 50 cur_align = iterator.next() 51 while cur_align: 52 fasta_align.add_sequence(cur_align.title, cur_align.sequence) 53 54 cur_align = iterator.next() 55 56 return fasta_align
57
58 -class FastaAlignment(Alignment):
59 """Work with the Fasta Alignment format. 60 61 The fasta alignment format is basically the same as the regular ol' 62 Fasta format we know and love, except the sequences have gaps 63 (represented by -'s). 64 """
65 - def __init__(self, alphabet = Alphabet.Gapped(IUPAC.ambiguous_dna)):
67
68 - def __str__(self):
69 """Print out a fasta version of the alignment info.""" 70 return_string = '' 71 for item in self._records: 72 new_f_record = Fasta.Record() 73 new_f_record.title = item.description 74 new_f_record.sequence = item.seq.data 75 76 return_string = return_string + str(new_f_record) + os.linesep + os.linesep 77 78 # have a extra newline, so strip two off and add one before returning 79 return return_string.rstrip() + os.linesep
80