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Shell Programming and Scripting
Perl to update field based on a specific set of rules
Post 303000872 by cmccabe on Friday 21st of July 2017 10:53:29 AM
07-21-2017
Code:
if ($FuncrefGene !~ /exonic/i) {
my ($transcript) = ($GeneDetailrefGene) =~ /(?:\.\d+[+*-]|\D)(\d+)/; # Get a numeric value if exists using (.) and (+/*/-) and capture digits into $transcript.
$transcript //= 0; # Give it a value of zero if no numeric value was found.
$classification = 'Likely Benign' if $transcript > 10; # Reclassify intronic variants (following c. nomenclature) to Likely Benign if distance greater than 10Code:
if ($FuncrefGene !~ /exonic/i) {
my ($transcript) = ($GeneDetailrefGene) =~ /(?:[+*-]d=)(\d+)/; # Get a numeric value if exists using (.) and (+/*/-) and capture digits into $transcript.
$transcript //= 0; # Give it a value of zero if no numeric value was found.
$classification = 'Likely Benign' if $transcript > 10; # Reclassify intronic variants (following c. nomenclature) to Likely Benign if distance greater than 10In line 1 f[8] is
NM_001134408:exon3:c.415-43A>G;NM_001134407:exon3:c.415-43A>G;NM_000833:exon4:c.415-43A>G
aand the ; (semi-colon) indicates the start of a new value. NM_001134408:exon3:c.415-43A>G would be the first value, so 43 is read into the $transcript variable and since f[13] is 0.0004, f[55] is VUS. Thank you
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LEARN ABOUT DEBIAN
ace::graphics::glyph::segments
Ace::Graphics::Glyph::segments(3pm) User Contributed Perl Documentation Ace::Graphics::Glyph::segments(3pm) NAME
Ace::Graphics::Glyph::segments - The "discontinuous segments" glyph SYNOPSIS
See L<Ace::Graphics::Panel> and L<Ace::Graphics::Glyph>. DESCRIPTION
This glyph draws a sequence feature that consists of multiple discontinuous segments, such as the exons on a transcript or a gapped alignment. The representation is a series of filled rectangles connected by line segments. The features passed to it must either respond to the Bio::SequenceFeatureI-style subSeqFeatures() method, or the AcePerl/Das-style segments() or merged_segments() methods. OPTIONS In addition to the common options, this glyph recognizes the b<-stranded> argument. If b<-stranded> is true and the feature is an alignment (has the target() method) then the glyph will draw little arrows in the segment boxes to indicate the direction of the alignment. BUGS
Please report them. SEE ALSO
Ace::Sequence, Ace::Sequence::Feature, Ace::Graphics::Panel, Ace::Graphics::Track, Ace::Graphics::Glyph::anchored_arrow, Ace::Graphics::Glyph::arrow, Ace::Graphics::Glyph::box, Ace::Graphics::Glyph::primers, Ace::Graphics::Glyph::segments, Ace::Graphics::Glyph::toomany, Ace::Graphics::Glyph::transcript, AUTHOR
Lincoln Stein <lstein@cshl.org>. Copyright (c) 2001 Cold Spring Harbor Laboratory This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. See DISCLAIMER.txt for disclaimers of warranty. perl v5.14.2 2001-09-17 Ace::Graphics::Glyph::segments(3pm)