bx.align.tools.thread module

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

bx.align.tools.thread.get_components_for_species(alignment, species)

Return the component for each species in the list species or None

bx.align.tools.thread.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

>>> print(threaded[1])
a score=0.0
s hg18.chr10 52730 69 + 135374737 GCAGGTACAATTCATCAAGAAAGGAATTACAACTTCAGAAATGTGTTCAAAATATATCCATACTTTGAC
s panTro1.chrUn_random 208115400 69 - 240967748 GCAGCTACTATTCATCAAGAAAGGGATTACAACTTCAGAAATGTGTTCAAAGTGTATCCATACTTTGAT