New package Phylip/Pars.pm

[cjfields]

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Author Name: Adam Witney (Adam Witney) Original Redmine Issue: 2988, https://redmine.open-bio.org/issues/2988 Original Date: 2010-01-13 Original Assignee: Bioperl Guts

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Addition of new package:

Bio/Tools/Run/Phylo/Phylip/Pars.pm

running Phylip’s pars

Pars.pm, Pars.t and test data file attached

This was created by modifying the already present Protpars.pm package and tests.

[cjfields]

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Original Redmine Comment Author Name: Adam Witney Original Date: 2010-01-13T11:00:43Z

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Created an attachment (id=1427) New Phylip/Pars.pm package

[cjfields]

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Original Redmine Comment Author Name: Adam Witney Original Date: 2010-01-13T11:01:52Z

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Created an attachment (id=1428) New Phylip/Pars.pm package test file

[cjfields]

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Original Redmine Comment Author Name: Adam Witney Original Date: 2010-01-13T11:02:35Z

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Created an attachment (id=1429) test data file

[cjfields]

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Original Redmine Comment Author Name: Jason Stajich Original Date: 2010-01-17T02:29:01Z

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I’m not sure where the submitted code is that I saw before in the emails, but there to allow other characters in alignments. I would rather say this needs to be done by subclassing validate_seq in your script or module. For example this is how I would encourage support allowing numbers (‘\d’) in alignments along with standard characters by having this in your script.

sub Bio::LocatableSeq::validateseq { my ($self,$seqstr) = @; if( ! defined $seqstr ){ $seqstr = $self->seq(); } return 0 unless( defined $seqstr); if((CORE::length($seqstr) > 0) && ($seqstr !~ /^([A-Za-z-.*\?\d]+)$/)) { $self->warn(“seq doesn’t validate, mismatch is ” . ($seqstr =~ /([^A-Za-z-.*\?\d]+)/g)); return 0; } return 1; }