7.3. IO functions

`bioconvert.io.maf`
`bioconvert.io.scf`

bioconvert.io.scf.read_from_buffer(f_file, length, offset)[source]: Return ‘length’ bits of file ‘f_file’ starting at offset ‘offset’

class bioconvert.io.maf.MAF(filename, outfile=None)[source]

A reader for MAF format.

Methods

count_insertions(alnString)

return length without insertion, forward and reverse shift

get_flag
to_sam

count_insertions(alnString)[source]: return length without insertion, forward and reverse shift

class bioconvert.io.maf.MAFLine(line)[source]

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.

Attributes:

alignment
alignment_size
alignment_start
mode
name
sequence_size
strand

Methods

get_alignment_length