annotate corebio/seq_io/fasta_io.py @ 9:f3462128e87c

Minor alterations to the galaxy interface with some better examples and error messages added.

#!/usr/bin/env python
 
#  Copyright (c) 2005 Gavin E. Crooks <[e-mail]>
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"""Read and write sequence information in FASTA format.
    
This is a very common format for unannotated biological sequence data, 
accepted by many multiple sequence alignment programs. Each sequence 
consists of a single-line description, followed by lines of sequence data. 
The first character of the description line is a greater-than (">") symbol 
in the first column. The first word of the description is often the name or 
ID of the sequence. Fasta files containing multiple sequences have one 
sequence listed right after another. 


Example Fasta File ::

>Lamprey GLOBIN V - SEA LAMPREY
PIVDTGSVA-P------------------LSAAEKTKIRSAWAPVYSTY---ETSGVDILVKFFTSTPAAQEFFPKFKGL
TT-----ADQLKKSA---DVRWHA-ERIINAVNDAVASMDDTEKMS--MKL-RDLSGKH----AKSFQV-----DPQYFK
VLAAVI-AD-TVAAGD--AGFEKLMSM------I---CILLR----S-----A-----Y------------
>Hagfish GLOBIN III - ATLANTIC HAGFISH
PITDHGQPP-T------------------LSEGDKKAIRESWPQIYKNF---EQNSLAVLLEFLKKFPKAQDSFPKFSAK
KS-------HLEQDP---AVKLQA-EVIINAVNHTIGLMDKEAAMK--KYL-KDLSTKH----STEFQV-----NPDMFK
ELSAVF-VS-TMG-GK--AAYEKLFSI------I---ATLLR----S-----T-----YDA----------
>Frog HEMOGLOBIN BETA CHAIN - EDIBLE FROG
----------GS-----------------------DLVSGFWGKV--DA---HKIGGEALARLLVVYPWTQRYFTTFGNL
GSADAIC-----HNA---KVLAHG-EKVLAAIGEGLKHPENLKAHY--AKL-SEYHSNK----LHVDPANFRLLGNVFIT
VLARHF-QH-EFTPELQ-HALEAHFCA------V---GDALA----K-----A-----YH-----------


"""
import re
from corebio.utils import *
from corebio.seq import *
from corebio.seq_io import *


names = ( 'fasta', 'pearson', 'fa')
extensions = ('fa', 'fasta', 'fast', 'seq', 'fsa', 'fst', 'nt', 'aa','fna','mpfa', 'faa', 'fnn','mfasta') 


example = """
>Lamprey GLOBIN V - SEA LAMPREY
PIVDTGSVA-P------------------LSAAEKTKIRSAWAPVYSTY---ETSGVDILVKFFTSTPAAQEFFPKFKGL
TT-----ADQLKKSA---DVRWHA-ERIINAVNDAVASMDDTEKMS--MKL-RDLSGKH----AKSFQV-----DPQYFK
VLAAVI-AD-TVAAGD--AGFEKLMSM------I---CILLR----S-----A-----Y------------

>Hagfish GLOBIN III - ATLANTIC HAGFISH
PITDHGQPP-T------------------LSEGDKKAIRESWPQIYKNF---EQNSLAVLLEFLKKFPKAQDSFPKFSAK
KS-------HLEQDP---AVKLQA-EVIINAVNHTIGLMDKEAAMK--KYL-KDLSTKH----STEFQV-----NPDMFK
ELSAVF-VS-TMG-GK--AAYEKLFSI------I---ATLLR----S-----T-----YDA----------

>Frog HEMOGLOBIN BETA CHAIN - EDIBLE FROG
----------GS-----------------------DLVSGFWGKV--DA---HKIGGEALARLLVVYPWTQRYFTTFGNL
GSADAIC-----HNA---KVLAHG-EKVLAAIGEGLKHPENLKAHY--AKL-SEYHSNK----LHVDPANFRLLGNVFIT
VLARHF-QH-EFTPELQ-HALEAHFCA------V---GDALA----K-----A-----YH-----------

"""    


def read(fin, alphabet=None): 
    """Read and parse a fasta file. 

    Args:
        fin -- A stream or file to read
        alphabet -- The expected alphabet of the data, if given
    Returns: 
        SeqList -- A list of sequences
    Raises: 
        ValueError -- If the file is unparsable
    """         
    seqs = [ s for s in iterseq(fin, alphabet)]
    name = names[0]
    if hasattr(fin, "name") : name = fin.name    
    return SeqList(seqs, name=name)


def readseq(fin, alphabet=None) :
    """Read one sequence from the file, starting 
    from the current file position."""
    return iterseq(fin, alphabet).next()
    
     
def iterseq(fin, alphabet=None):
    """ Parse a fasta file and generate sequences.
    
    Args:
        fin -- A stream or file to read
        alphabet -- The expected alphabet of the data, if given    
    Yeilds: 
        Seq -- One alphabetic sequence at a time.
    Raises: 
        ValueError -- If the file is unparsable
    """
    alphabet = Alphabet(alphabet)

    seqs = []
    comments = []   # FIXME: comments before first sequence are lost.
    header = None
    header_lineno = -1
    
    def build_seq(seqs,alphabet, header, header_lineno,comments) :
        try :
            name = header.split(' ',1)[0]
            if comments :
                header += '\n' + '\n'.join(comments)
            s = Seq( "".join(seqs), alphabet, name=name, description=header)
        except ValueError:
             raise ValueError(
                "Parsed failed with sequence starting at line %d: "
                "Character not in alphabet: %s" % (header_lineno, alphabet) )
        return s

    for lineno, line in enumerate(fin) :
        line = line.strip()
        if line == '' : continue
        if line.startswith('>') :
            if header is not None :
                yield  build_seq(seqs,alphabet, header, header_lineno, comments)
                header = None
                seqs = []
            header = line[1:]
            header_lineno = lineno
            comments = []
        elif line.startswith(';') : 
            # Optional (and unusual) comment line
            comments.append(line[1:])           
        else :
            if header is None :
                raise ValueError (
                    "Parse failed on line %d: sequence before header"  
                    % (lineno) )
            seqs.append(line)    

    if not seqs: return
    yield build_seq(seqs,alphabet, header, header_lineno, comments)

     
def write(fout, seqs): 
    """Write a fasta file. 

    Args:
        fout -- A writable stream.
        seqs  -- A list of Seq's
    """ 
    if seqs.description :
        for line in seqs.description.splitlines():
            print >>fout, ';'+ line        
    for s in seqs :
        writeseq(fout, s)

    
def writeseq(afile, seq):
    """ Write a single sequence in fasta format.

    Args:
        afile -- A writable stream.
        seq  -- A Seq instance
    """

    header = seq.description or seq.name or ''
    
    # We prepend '>' to the first header line
    # Additional lines start with ';' to indicate comment lines
    if header :
        header = header.splitlines()  
        print >>afile, '>'+header[0]
        if len(header) > 1 :
            for h in header[1:] :
                print >>afile, ';' +h
    else :
        print >>afile, '>'
    
    L = len(seq) 
    line_length = 80
    for n in range (1+ L/line_length) :
        print >>afile, seq[n * line_length: (n+1) * line_length] 
    print >>afile
    
    
def index(afile, alphabet=None) :
    """Return a FileIndex for the fasta file. Sequences can be retrieved
    by item number or name.
    """
    def parser( afile) :
        return readseq(afile, alphabet)
    
    key = re.compile(r"^>\s*(\S*)")
    def linekey( line):
        k = key.search(line)
        if k is None : return None
        return k.group(1)
        
    return FileIndex(afile, linekey, parser)