root/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-macosx-10.6-universal-ucs2.egg/bx/seq/core.py

"""
Support for "biological sequence" files.

:Author: Bob Harris (rsharris@bx.psu.edu)

See seq.py for more information
"""

import struct
import fasta, nib, qdna

# DNA reverse complement table

DNA_COMP = "                                             -                  " \
           " TVGH  CD  M KN   YSA BWXR       tvgh  cd  m kn   ysa bwxr      " \
           "                                                                " \
           "                                                                "

def reverse_complement( text ):
    return text.translate(DNA_COMP)[::-1]


def seq_file (file, format=None, revcomp=False, name="", gap=None, contig=None):
    if (format == None): format = infer_format(file)
    if (contig != None) and (format not in ["fasta",None]):
        raise "Contigs are not supported for format %s" % format
    if   (format == "fasta"): return fasta.FastaFile (file, revcomp=revcomp, name=name, gap=gap, contig=contig)
    elif (format == "nib"):   return nib.NibFile     (file, revcomp=revcomp, name=name, gap=gap)
    elif (format == "qdna"):  return qdna.QdnaFile   (file, revcomp=revcomp, name=name, gap=gap)
    else:
        if (format == None): format = ""
        else:                format = " " + format
        raise "Unknown sequence format%s in %s" % (format,file.name)


def seq_reader (file, format=None, revcomp=False, name="", gap=None):
    if   (format == None):    format = infer_format(file)
    if   (format == "fasta"): return fasta.FastaReader (file, revcomp=revcomp, name=name, gap=gap)
    elif (format == "nib"):   return nib.NibReader     (file, revcomp=revcomp, name=name, gap=gap)
    elif (format == "qdna"):  return qdna.QdnaReader   (file, revcomp=revcomp, name=name, gap=gap)
    else: raise "Unknown sequence format %s" % format


def seq_writer (outfile, format=None, name=""):
    if   (format == "fasta"): return fasta.FastaWriter (outfile)
    elif (format == "nib"):   return nib.NibWriter     (outfile)
    elif (format == "qdna"):  return qdna.QdnaWriter   (outfile)
    else: raise "Unknown sequence format %s" % format


def infer_format (file):
    format = None
    magic = struct.unpack(">L", file.read(4))[0]
    if (magic == nib.NIB_MAGIC_NUMBER) or (magic == nib.NIB_MAGIC_NUMBER_SWAP):
        format = "nib"
    elif (magic == qdna.qdnaMagic) or (magic == qdna.qdnaMagicSwap):
        format = "qdna"
    else:
        file.seek(0)
        if (file.read(1) == ">"):
            format = "fasta"
    file.seek(0)
    return format