Commit 3c97511c authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
Browse files

Beeeep! Change alignment model to ungapped from affine:local.

Bigger penalty for exonerate matches on other seq_regions.

Rescore penalty altered to 0.9.
parent c293d594
......@@ -468,16 +468,16 @@ sub run_exonerate {
# run exonerate jobs using lsf
#
my $exonerate_job =
qq{$exonerate_path }
. qq{--query $source_file --target $target_file }
. q{--querychunkid $LSB_JOBINDEX }
. qq{--querychunktotal $num_jobs }
. q{--model affine:local -M 900 --showalignment FALSE --subopt no }
. qq{--percent $percent }
. $self->conf->param('exonerate_extra_params') . " "
. q{--ryo 'myinfo: %qi %ti %et %ql %tl\n' }
. qq{| grep '^myinfo:' > $dump_path/exonerate_map.\$LSB_JOBINDEX}
. "\n";
qq{$exonerate_path } .
qq{--query $source_file --target $target_file } .
q{--querychunkid $LSB_JOBINDEX } .
qq{--querychunktotal $num_jobs } .
q{--model ungapped -M 1000 -D 100 } .
q{--showalignment FALSE --subopt no } . qq{--percent $percent } .
$self->conf->param('exonerate_extra_params') . " " .
q{--ryo 'myinfo: %qi %ti %et %ql %tl\n' } .
qq{| grep '^myinfo:' > $dump_path/exonerate_map.\$LSB_JOBINDEX} .
"\n";
$self->logger->info("Submitting $num_jobs exonerate jobs to lsf.\n");
$self->logger->debug("$exonerate_job\n\n");
......@@ -720,7 +720,10 @@ sub parse_exonerate_results {
if ( $source_sr ne $target_sr ) {
# PENALTY: The target and source are not on the same
# seq_region.
$score *= 0.75;
$score *= 0.70;
# With a penalty of 0.7, exonerate scores need to be above
# approximately 0.714 to make the 0.5 threshold.
++$penalised;
}
......@@ -810,7 +813,7 @@ sub non_mapped_transcript_rescore {
# PENALTY: The exon appears to belong to a transcript that has not
# been mapped.
$matrix->set_score( $entry->source(), $entry->target(),
0.8*$entry->score() );
0.9*$entry->score() );
$i++;
}
} ## end foreach my $entry ( @{ $matrix...})
......
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