bx.align.tools.fuse module

Tools for fusing contiguous alignment blocks together.

class bx.align.tools.fuse.FusingAlignmentWriter(maf_writer)

Bases: object

Wrapper for an alignment Writer which attempts to fuse adjacent blocks

close()

write(m)

bx.align.tools.fuse.fuse(m1, m2)

Attempt to fuse two blocks. If they can be fused returns a new block, otherwise returns None.

Example:

>>> import bx.align.maf

>>> block1 = bx.align.maf.from_string( '''
... a score=0.0
... s hg18.chr10 52686 44 + 135374737 GTGCTAACTTACTGCTCCACAGAAAACATCAATTCTGCTCATGC
... i hg18.chr10 N 0 C 0
... s panTro1.chrUn_random 208115356 44 - 240967748 GTGCTAACTGACTGCTCCAGAGAAAACATCAATTCTGTTCATGT
... ''' )

>>> block2 = bx.align.maf.from_string( '''
... a score=0.0
... s hg18.chr10 52730 69 + 135374737 GCAGGTACAATTCATCAAGAAAGGAATTACAACTTCAGAAATGTGTTCAAAATATATCCATACTTTGAC
... i hg18.chr10 C 0 I 12
... s panTro1.chrUn_random 208115400 69 - 240967748 GCAGCTACTATTCATCAAGAAAGGGATTACAACTTCAGAAATGTGTTCAAAGTGTATCCATACTTTGAT
... ''' )

>>> fused = fuse( block1, block2 )

>>> print(fused)
a score=0.0
s hg18.chr10 52686 113 + 135374737 GTGCTAACTTACTGCTCCACAGAAAACATCAATTCTGCTCATGCGCAGGTACAATTCATCAAGAAAGGAATTACAACTTCAGAAATGTGTTCAAAATATATCCATACTTTGAC
i hg18.chr10 N 0 I 12
s panTro1.chrUn_random 208115356 113 - 240967748 GTGCTAACTGACTGCTCCAGAGAAAACATCAATTCTGTTCATGTGCAGCTACTATTCATCAAGAAAGGGATTACAACTTCAGAAATGTGTTCAAAGTGTATCCATACTTTGAT

bx.align.tools.fuse.fuse_list(mafs): Try to fuse a list of blocks by progressively fusing each adjacent pair.