7.3. IO functions

bioconvert.io.maf
bioconvert.io.scf

read_from_buffer(f_file, length, offset)

Return 'length' bits of file 'f_file' starting at offset 'offset'

class MAF(filename, outfile=None)

A reader for MAF format.

count_insertions(alnString)

return length without insertion, forward and reverse shift

class MAFLine(line)

A reader for MAF format.

mode refname start algsize strand refsize alignment

a
s ref    100 10 + 100000 ---AGC-CAT-CATT
s contig 0   10 + 10     ---AGC-CAT-CATT

a
s ref    100 12 + 100000 ---AGC-CAT-CATTTT
s contig 0   12 + 12     ---AGC-CAT-CATTTT

The alignments are stored by pair, one item for the reference, one for the query. The query (second line) starts at zero.