bx.align.lav module

Support for reading and writing the LAV format produced by the blastz pairwise aligner.

class bx.align.lav.LavAsPiecesReader(file, path_subs=None, fail_to_ns=False)

Bases: Reader

Iterate over all lav blocks in a file in order, returning alignments as score and pieces, as returned by Reader.parse_a_stanza

build_alignment(score, pieces)

converts a score and pieces to an alignment

class bx.align.lav.Reader(file, path_subs=None, fail_to_ns=False)

Bases: object

Iterate over all lav blocks in a file in order

build_alignment(score, pieces)

converts a score and pieces to an alignment

close()

close_seqs()

d_stanza()

fetch_line(strip=True, requireLine=True, report='')

h_stanza()

header_to_src_name(header)

open_seqs()

parse_a_stanza()

returns the pair (score,pieces) where pieces is a list of ungapped segments (start1,start2,length,pctId) with start1,start2 origin-0

parse_h_stanza()

parse_s_seq(line)

parse_s_stanza()

parse_unknown_stanza()

path_to_src_name(path_name)

s_stanza()

class bx.align.lav.ReaderIter(reader)

Bases: object

class bx.align.lav.Writer(file, attributes=None)

Bases: object

close()

write(alignment)

write_a_stanza(alignment)

write_h_stanza()

write_lav_marker()

write_s_stanza()

write_trailer()

bx.align.lav.build_filename(fmt, src)

bx.align.lav.chrom_key(src)

bx.align.lav.do_path_subs(path, path_subs)

bx.align.lav.minus_or_nothing(strand)

bx.align.lav.rc_or_nothing(strand)

bx.align.lav.sort_keys_by_chrom(keys)