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mavis.blat

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

mavis.blat.Blat.millibad()

this function is used in calculating percent identity direct translation of the perl code

https://genome.ucsc.edu/FAQ/FAQblat.html#blat4

@staticmethod
def millibad(row, is_protein=False, is_mrna=True):

Args

  • row
  • is_protein
  • is_mrna

mavis.blat.Blat.score()

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)

@staticmethod
def score(row, is_protein=False):

Args

  • row
  • is_protein

mavis.blat.Blat.pslx_row_to_pysam()

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

@staticmethod
def pslx_row_to_pysam(row, bam_cache, reference_genome):

Args

  • row
  • bam_cache (BamCache): the bam file/cache to use as a template for creating reference_id from chr name

mavis.blat.process_blat_output()

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

def 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,
):

Args

  • input_bam_cache
  • query_id_mapping
  • reference_genome
  • aligner_output_file
  • blat_min_percent_of_max_score
  • blat_min_identity
  • blat_limit_top_aln
  • is_protein