Bio-Polloc
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--version
--wordexp
Shell options:
-irsD or -c command or -O shopt_option (invocation only)
-abefhkmnptuvxBCHP or -o option
--------------------- WARNING ---------------------
MSG: Muscle call crashed: 512 [command -in /tmp/_YS2FojZj7 -out /tmp/7BP7tE2dKG/fwsAmEh1NG 2> /dev/null]
---------------------------------------------------
Can't call method "average_percentage_identity" on an undefined value at /Users/luismrodriguezr/.cpan/build/Bio::Polloc-1.0503-xA5_RC/blib/lib/Bio/Polloc/LociGroup.pm line 376.
# Looks like you planned 13 tests but ran 6.
# Looks like your test exited with 2 just after 6.
t/05-typing/02-typing.t ............ Dubious, test returned 2 (wstat 512, 0x200)
Failed 7/13 subtests
```
This very verbose message often means one thing: you have `Bio::Tools::Run::Alignment::Muscle` installed in
your system, but you don't have Muscle. The solution is pretty easy: install muscle, available at
[Robert Edgar's website](http://www.drive5.com/muscle/downloads.htm).
--version
--wordexp
Shell options:
-irsD or -c command or -O shopt_option (invocation only)
-abefhkmnptuvxBCHP or -o option
--------------------- WARNING ---------------------
MSG: Muscle call crashed: 512 [command -in /tmp/_YS2FojZj7 -out /tmp/7BP7tE2dKG/fwsAmEh1NG 2> /dev/null]
---------------------------------------------------
Can't call method "average_percentage_identity" on an undefined value at /Users/luismrodriguezr/.cpan/build/Bio::Polloc-1.0503-xA5_RC/blib/lib/Bio/Polloc/LociGroup.pm line 376.
# Looks like you planned 13 tests but ran 6.
# Looks like your test exited with 2 just after 6.
t/05-typing/02-typing.t ............ Dubious, test returned 2 (wstat 512, 0x200)
Failed 7/13 subtests
```
This very verbose message often means one thing: you have `Bio::Tools::Run::Alignment::Muscle` installed in
your system, but you don't have Muscle. The solution is pretty easy: install muscle, available at
[Robert Edgar's website](http://www.drive5.com/muscle/downloads.htm).
lib/Bio/Polloc/GroupCriteria.pm view on Meta::CPAN
sequences).
=back
=item -score I<int>
Minimum score for either algorithms B<blast> and B<hmmer>. 20 by default.
=item -consensusperc I<float>
Minimum percentage a residue must appear in order to include it in the
consensus used as query. 60 by default. Only if -algorithm blast.
=item -e I<float>
If C<-algorithm> B<blast>, maximum e-value. 0.1 by default.
=item -p I<str>
If C<-algorithm> B<blast>, program used (C<[t]blast[npx]>). B<blastn> by
default.
lib/Bio/Polloc/GroupCriteria/operator/num.pm view on Meta::CPAN
my $factory = Bio::Tools::Run::Alignment::Muscle->new();
$factory->quiet(1);
UNIVERSAL::can($o1, 'isa') or $self->throw('First operator must be an object', $o1);
UNIVERSAL::can($o2, 'isa') or $self->throw('First operator must be an object', $o2);
$o1->isa('Bio::Seq') or $self->throw('First operator must be a Bio::Seq object', $o1);
$o2->isa('Bio::Seq') or $self->throw('Second operator must be a Bio::Seq object', $o2);
$o1->id('op1');
$o2->id('op2');
my $aln = $factory->align([$o1, $o2]);
my $out = 0;
$out = ($ret eq 'sim') ? $aln->overall_percentage_identity('long')/100 : $aln->score;
$factory->cleanup(); # This is to solve the issue #1
defined $out or $self->throw('Empty value for '.$ret, $self, 'Bio::Polloc::Polloc::UnexpectedException');
return $out;
}
$self->throw("Unknown numeric operation", $self->operation);
}
=head1 INTERNAL METHODS
Methods intended to be used only within the scope of Bio::Polloc::*
lib/Bio/Polloc/LociGroup.pm view on Meta::CPAN
#Â Compare
LOCUS: for my $k (0 .. $#{$self->loci}){
my $tgt = Bio::Polloc::GroupCriteria->_build_subseq(
$self->loci->[$k]->seq,
$self->loci->[$k]->from-$size,
$self->loci->[$k]->to+$size);
next LOCUS unless $tgt; # <- This may be way too paranoic!
$tgt->id('tgt');
my $tgtrc = $tgt->revcom;
$self->debug("Setting strand for ".$self->loci->[$k]->id) if defined $self->loci->[$k]->id;
my $eval_fun = 'average_percentage_identity';
#$eval_fun = 'overall_percentage_identity';
if($factory->align([$ref, $tgt])->$eval_fun
< $factory->align([$ref,$tgtrc])->$eval_fun){
$self->debug("Assuming negative strand, setting locus orientation");
$self->loci->[$k]->strand('-');
}else{
$self->debug("Assuming positive strand, setting locus orientation");
$self->loci->[$k]->strand('+');
}
} # LOCUS
}
lib/Bio/Polloc/Locus/amplicon.pm view on Meta::CPAN
$self->{'_rev_primer'} = $value if defined $value;
return $self->{'_rev_primer'};
}
=head2 score
Gets the score
=head3 Returns
The score (float or undef). As the percentage of the primers
matching the target sequence.
=cut
sub score {
my($self,$value) = @_;
$self->warn("Trying to set value via read-only method 'score()'") if defined $value;
return 100 - 100 * ($self->errors || 0) * (
$self->fwd_primer and $self->rev_primer ?
1/length $self->fwd_primer . $self->rev_primer : 1);
lib/Bio/Polloc/Locus/composition.pm view on Meta::CPAN
=head3 Arguments
=over
=item -letters I<str>
The residues
=item -composition I<float>
The percentage of the sequence covered by the residues (letters).
=back
=cut
sub new {
my($caller,@args) = @_;
my $self = $caller->SUPER::new(@args);
$self->_initialize(@args);
return $self;
lib/Bio/Polloc/Locus/composition.pm view on Meta::CPAN
sub letters {
my($self,$value) = @_;
$self->{'_letters'} = $value if defined $value;
return $self->{'_letters'};
}
=head2 composition
Gets/sets the percentage of the sequence covered by the residues (letters).
=head3 Arguments
The percentage (float, optional).
=head3 Returns
The percentage (float or undef).
=cut
sub composition {
my($self,$value) = @_;
$self->{'_composition'} = $value if defined $value;
return $self->{'_composition'};
}
lib/Bio/Polloc/Locus/repeat.pm view on Meta::CPAN
=item -period I<float>
The period of the repeat (units length).
=item -exponent I<float>
The exponent (No of units).
=item -error I<float>
Mismatches percentage.
=item -repeats I<str>
Repetitive sequences, repeats space-separated.
=item -consensus I<str>
Repeats consensus.
=back
lib/Bio/Polloc/Locus/repeat.pm view on Meta::CPAN
=cut
sub consensus {
my($self,$value) = @_;
$self->{'_consensus'} = $value if defined $value;
return $self->{'_consensus'};
}
=head2 error
Gets/sets the error rate of the repeat. I<I.e.>, the percentage of mismatches.
=head3 Arguments
The error (float).
=head3 Returns
The error (float or undef).
=cut
lib/Bio/Polloc/Rule/composition.pm view on Meta::CPAN
Residues (str or undef)
=cut
sub letters { shift->_search_value("letters", shift) }
=head2 min_perc
Sets/gets the minimum percentage
=head2 Arguments
Percentage (float, optional)
=head2 Returns
Percentage (float or undef)
=cut
sub min_perc { shift->_search_value("min_perc", shift) }
=head2 max_perc
Sets/gets the maximum percentage
=head2 Arguments
Percentage (float, optional)
=head2 Returns
Percentage (float or undef)
=cut
lib/Bio/Polloc/Rule/composition.pm view on Meta::CPAN
=item -letters
The residues to take into account as a string
=item -range
The allowed (perc.) range in the format 20..50
=item -min_perc
The minimum percentage (ignored if range is set)
=item -max_perc
The maximum percentage (ignored if range is set)
=back
=head2 Returns
Value (ref-to-hash or undef)
=cut
sub _qualify_value {
lib/Bio/Polloc/Rule/repeat.pm view on Meta::CPAN
=item -allowsmall I<bool (int)>
If true, allows spurious results
=item -win I<float>
Process by sliding windows of size C<2*n> overlaping by C<n>
=item -minsim I<float>
Minimum similarity percent
=item -maxsim I<float>
Maximum similarity percent
=back
=head3 Return
Value (I<hashref> or C<undef>).
=head1 INTERNAL METHODS
Methods intended to be used only within the scope of Bio::Polloc::*
lib/Bio/Polloc/Rule/tandemrepeat.pm view on Meta::CPAN
# And finally parse it
my $ontable = 0;
my @feats = ();
$run = Bio::Polloc::Polloc::IO->new(-file=>$outfile);
while(my $line = $run->_readline){
if($line =~ m/^Parameters:\s/){
$ontable = 1;
}elsif($ontable){
chomp $line;
next if $line =~ /^\s*$/;
#from to period-size copy-number consensus-size percent-matches percent-indels score A T C G entropy consensus sequence
#269 316 18 2.6 19 56 3 51 8 45 35 10 1.68 GTCGCGGCCACGTGCACCC GTCGCGTCCACGTGCGCCCGAGCCGGC...
my @v = split /\s+/, $line;
$#v==14 or $self->throw("Unexpected line $.",$line,"Bio::Polloc::Polloc::ParsingException");
# MINSIZE MAXSIZE MINPERIOD MAXPERIOD EXP MATCH MISMATCH INDELS MINSCORE MAXSCORE
$self->debug("Checking additional parameters");
next if length($v[14]) > $c_v{'maxsize'} or length($v[14]) < $c_v{'minsize'};
next if $v[2] > $c_v{'maxperiod'} or $v[2] < $c_v{'minperiod'};
next if $v[3] < $c_v{'exp'};
next if $v[7] < $c_v{'minscore'};
next if $c_v{'maxscore'} and $v[7] > $c_v{'maxscore'};
lib/Bio/Polloc/Rule/tandemrepeat.pm view on Meta::CPAN
=item -minscore I<float>
Minimum score
=item -maxscore I<float>
Maximum score
=item -minsim I<float>
Minimum similarity percent
=item -maxsim I<float>
Maximum similarity percent
=item -pm I<float>
Match probability
=item -pi I<float>
Indel probability
=back
lib/Bio/Polloc/Typing/bandingPattern/amplification.pm view on Meta::CPAN
sub flanking_size {
my($self, $value) = @_;
$self->{'_flanking_size'} = $value+0 if defined $value;
return 500 unless defined $self->{'_flanking_size'};
return $self->{'_flanking_size'};
}
=head2 annealing_errors
Gets/sets the maximum percentage of errors allowed for a primer to anneal.
0 by default.
=cut
sub annealing_errors {
my($self, $value) = @_;
$self->{'_annealing_errors'} = $value+0 if defined $value;
return $self->{'_annealing_errors'} || 0;
}
scripts/polloc_primers.pl view on Meta::CPAN
Example: C<"/tmp/polloc-primers.out">.
=item Draw
Should I produce graphical output? Any non-empty string to
generate PNG images, or empty string (C<''>) to ignore graphical
output.
=item Consensus (I<float>)
Consensus percentage for primers design.
Default: C<100>.
=item Length (I<int>)
Length of the primers.
Default: C<20>.
=item Errors (I<int>)
scripts/polloc_vntrs.pl view on Meta::CPAN
}
sub _advance_proto($$) {
my($file, $msg) = @_;
open ADV, ">", $file or die "I can not open the '$file' file: $!\n";
print ADV $msg;
close ADV;
}
sub csv_header() {
return "ID\tGenome\tSeq\tFrom\tTo\tUnit length\tCopy number\tMismatch percent\tScore\t".
"Left 500bp\tRight 500bp (rc)\tRepeats\tConsensus/Notes\n";
}
sub csv_line($$) {
my $f = shift;
my $n = shift;
$n||= '';
my $left = $f->seq->subseq(max(1, $f->from-500), $f->from);
my $right = Bio::Seq->new(-seq=>$f->seq->subseq($f->to, min($f->seq->length, $f->to+500)));
$right = $right->revcom->seq;
my $seq;
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