root/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-macosx-10.6-universal-ucs2.egg/bx/align/tools/thread.py

"""
Tools for "threading" out specific species from alignments (removing other
species and fixing alignment text).
"""

import sys
from itertools import *
from copy import deepcopy

def thread( mafs, species ):
    """
    Restrict an list of alignments to a given list of species by:
    
        1) Removing components for any other species 
        2) Remove any columns containing all gaps
      
    Example:
      
    >>> import bx.align.maf
      
    >>> block1 = bx.align.maf.from_string( '''
    ... a score=4964.0
    ... s hg18.chr10                  52686 44 + 135374737 GTGCTAACTTACTGCTCCACAGAAAACATCAATTCTGCTCATGC
    ... s rheMac2.chr20            58163346 43 -  88221753 ATATTATCTTAACATTAAAGA-AGAACAGTAATTCTGGTCATAA
    ... s panTro1.chrUn_random    208115356 44 - 240967748 GTGCTAACTGACTGCTCCAGAGAAAACATCAATTCTGTTCATGT
    ... s oryCun1.scaffold_175207     85970 22 +    212797 ----------------------AAAATATTAGTTATCACCATAT
    ... s bosTau2.chr23            23894492 43 +  41602928 AAACTACCTTAATGTCACAGG-AAACAATGTATgctgctgctgc
    ... ''' )
    
    >>> block2 = bx.align.maf.from_string( '''
    ... a score=9151.0
    ... s hg18.chr10                  52730 69 + 135374737 GCAGGTACAATTCATCAAGAAAG-GAATTACAACTTCAGAAATGTGTTCAAAATATATCCATACTT-TGAC
    ... s oryCun1.scaffold_175207     85992 71 +    212797 TCTAGTGCTCTCCAATAATATAATAGATTATAACTTCATATAATTATGTGAAATATAAGATTATTTATCAG
    ... s panTro1.chrUn_random    208115400 69 - 240967748 GCAGCTACTATTCATCAAGAAAG-GGATTACAACTTCAGAAATGTGTTCAAAGTGTATCCATACTT-TGAT
    ... s rheMac2.chr20            58163389 69 -  88221753 ACACATATTATTTCTTAACATGGAGGATTATATCTT-AAACATGTGTGCaaaatataaatatatat-tcaa
    ... ''' )
    
    >>> mafs = [ block1, block2 ]
    
    >>> threaded = [ t for t in thread( mafs, [ "hg18", "panTro1" ] ) ]
    
    >>> len( threaded )
    2
    
    >>> print threaded[0]
    a score=0.0
    s hg18.chr10 52686 44 + 135374737 GTGCTAACTTACTGCTCCACAGAAAACATCAATTCTGCTCATGC
    s panTro1.chrUn_random 208115356 44 - 240967748 GTGCTAACTGACTGCTCCAGAGAAAACATCAATTCTGTTCATGT
    <BLANKLINE>

    >>> print threaded[1]
    a score=0.0
    s hg18.chr10 52730 69 + 135374737 GCAGGTACAATTCATCAAGAAAGGAATTACAACTTCAGAAATGTGTTCAAAATATATCCATACTTTGAC
    s panTro1.chrUn_random 208115400 69 - 240967748 GCAGCTACTATTCATCAAGAAAGGGATTACAACTTCAGAAATGTGTTCAAAGTGTATCCATACTTTGAT
    <BLANKLINE>
    
    """
    for m in mafs:
        new_maf = deepcopy( m )
        new_components = get_components_for_species( new_maf, species ) 
        if new_components: 
            remove_all_gap_columns( new_components )          
            new_maf.components = new_components
            new_maf.score = 0.0
            new_maf.text_size = len(new_components[0].text)
            yield new_maf
        
def get_components_for_species( alignment, species ):
    """Return the component for each species in the list `species` or None"""
    # If the number of components in the alignment is less that the requested number
    # of species we can immediately fail
    if len( alignment.components ) < len( species ): return None
    # Otherwise, build an index of components by species, then lookup 
    index = dict( [ ( c.src.split( '.' )[0], c ) for c in alignment.components ] )
    try: return [ index[s] for s in species ]
    except: return None

def remove_all_gap_columns( components ):
    """
    Remove any columns containing only gaps from a set of alignment components,
    text of components is modified IN PLACE.
    
    TODO: Optimize this with Pyrex.
    """        
    seqs = [ list( c.text ) for c in components ]
    i = 0
    text_size = len( seqs[0] )
    while i < text_size:
        all_gap = True
        for seq in seqs:
            if seq[i] != '-': all_gap = False
        if all_gap:
            for seq in seqs: del seq[i]
            text_size -= 1
        else:
            i += 1
    for i in range( len( components ) ):
        components[i].text = ''.join( seqs[i] )