blat module

In general the coordinates in psl files are “zero based half open.” The first base in a sequence is numbered
zero rather than one. When representing a range the end coordinate is not included in the range. Thus the first
100 bases of a sequence are represented as 0-100, and the second 100 bases are represented as 100-200. There is
another little unusual feature in the .psl format. It has to do with how coordinates are handled on the
negative strand. In the qStart/qEnd fields the coordinates are where it matches from the point of view of the forward
strand (even when the match is on the reverse strand). However on the qStarts[] list, the coordinates are reversed.

– http://wiki.bits.vib.be/index.php/Blat

class mavis.blat.Blat

Bases: object

static millibad(row, is_protein=False, is_mrna=True)

this function is used in calculating percent identity direct translation of the perl code # https://genome.ucsc.edu/FAQ/FAQblat.html#blat4

static percent_identity(row, is_protein=False, is_mrna=True)

static pslx_row_to_pysam(row, bam_cache, reference_genome)

given a ‘row’ from reading a pslx file. converts the row to a BlatAlignedSegment object

Parameters:

• row (dict of str) – a row object from the ‘read_pslx’ method
• bam_cache (BamCache) – the bam file/cache to use as a template for creating reference_id from chr name
• reference_genome (dict of Bio.SeqRecord by str) – dict of reference sequence by template/chr name

static read_pslx(filename, seqid_to_sequence_mapping, is_protein=False, verbose=True)

static score(row, is_protein=False)

direct translation from ucsc guidelines on replicating the web blat score https://genome.ucsc.edu/FAQ/FAQblat.html#blat4

below are lines from the perl code i’ve re-written in python

my $sizeMul = pslIsProtein($blockCount, $strand, $tStart, $tEnd, $tSize, $tStarts, $blockSizes);
sizmul = 1 for DNA
my $pslScore = $sizeMul * ($matches + ($repMatches >> 1) ) - $sizeMul * $misMatches - $qNumInsert - $tNumIns
    ert)

mavis.blat.get_blat_version()

executes a subprocess to try and run blat and parse the version number from the output

Example

>>> get_blat_version()
'36x2'

mavis.blat.process_blat_output(input_bam_cache, query_id_mapping, reference_genome, aligner_output_file='aligner_out.temp', blat_min_percent_of_max_score=0.8, blat_min_identity=0.7, blat_limit_top_aln=25, is_protein=False)

converts the blat output pslx (unheadered file) to bam reads