Bio-MUST-Apps-HmmCleaner
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bin/HmmCleaner.pl view on Meta::CPAN
#!/usr/bin/env perl
# PODNAME: HmmCleaner.pl
# ABSTRACT: Removing low similarity segments from your MSA
use Modern::Perl;
use Getopt::Euclid;
## no critic (RequireLocalizedPunctuationVars)
BEGIN{
$ENV{Smart_Comments} = $ARGV{-v}
? join q{ }, map { '#' x (2 + $_) } 1..$ARGV{-v}
: q{}
;
}
## use critic
use Smart::Comments -ENV;
use Bio::MUST::Apps::HmmCleaner;
use aliased 'Bio::MUST::Apps::HmmCleaner';
### Lauching script...
###### %ARGV
my %costs_values = (
'default' => [-0.15, -0.08, 0.15, 0.45],
'large' => [-0.175, -0.04, 0.15, 0.4],
'specificity' => [-0.125, -0.07, 0.175, 0.4],
'large_specificity' => [-0.125, -0.03, 0.15, 0.4],
);
my $costs = $costs_values{'default'};
$costs = $costs_values{'large'} if ($ARGV{'--large'});
$costs = $costs_values{'specificity'} if ($ARGV{'--specificity'});
$costs = $costs_values{'large_specificity'} if ( $ARGV{'--large'} && $ARGV{'--specificity'});
$costs = [$ARGV{'-costs'}{'c1'}, $ARGV{'-costs'}{'c2'}, $ARGV{'-costs'}{'c3'}, $ARGV{'-costs'}{'c4'}] if ($ARGV{'-costs'});
#### $costs
for my $file ( @{$ARGV{'<infiles>'}} ) {
my $args = {
ali => $file,
ali_model => $file,
threshold => 1,
changeID => $ARGV{'--changeID'},
#~ delchar => $ARGV{'-delchar'},
costs => $costs,
consider_X => ($ARGV{'--noX'}) ? 0 : 1,
perseq_profile => ($ARGV{'-profile'} eq 'leave-one-out') ? 1 : 0,
outfile_type => ($ARGV{'--ali'}) ? 1 : 0,
debug_mode => ($ARGV{'-v'}>5) ? 1 : 0,
symfrac => $ARGV{'-symfrac'},
};
### Creating object for file : $file
my $cleaner = HmmCleaner->new($args);
($ARGV{'--log_only'}) ? $cleaner->store_log : $cleaner->store_all;
}
### End of script...
__END__
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