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lib/Bio/AutomatedAnnotation/Prokka.pm view on Meta::CPAN
if (m/^>(\S+)/) {
$sid = $1;
next;
}
my @x = split m/\s+/;
next unless @x == 5 and $x[0] =~ m/^\d+$/;
# and $x[4] =~ m/^\([ATCG]{3}\)$/i;
#$self->msg($_);
$self->msg("@x");
lib/Bio/AutomatedAnnotation/Prokka.pm view on Meta::CPAN
$self->msg("Running: $cmd");
my $tool = "SignalP:" . $tools{signalp}->{VERSION};
my $num_sigpep = 0;
open SIGNALP, "$cmd |";
while (<SIGNALP>) {
my @x = split m/\s+/;
if ( $sigpver == 3 ) {
next unless @x == 7 and $x[6] eq 'Y'; # has sig_pep
my $parent = $cds{ $x[0] };
my $prob = $x[5];
my $cleave = $x[3];
lib/Bio/AutomatedAnnotation/Prokka.pm view on Meta::CPAN
my $bls = Bio::SearchIO->new( -file => "$tempdir/$pid.seq.out", -format => $db->{FMT}, -version => $db->{VERSION} );
my $res = $bls->next_result or next;
my $hit = $res->next_hit or next;
my ( $prod, $gene, $EC ) = ( $hit->description, '', '' );
if ( $prod =~ m/~~~/ ) {
( $EC, $gene, $prod ) = split m/~~~/, $prod;
$EC =~ s/n\d+/-/g; # collapse transitionary EC numbers
}
my $cleanprod = $prod;
if ( $self->cleanup_prod ) {
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lib/Bio/BioStudio/BLAST.pm view on Meta::CPAN
{
open (my $BLASTINDEX, '<', $indexpath)
|| croak "BS_ERROR: Can't open BLAST index $indexpath : $OS_ERROR";
my $indexref = do {local $/ = <$BLASTINDEX>};
close $BLASTINDEX;
my @indexkeys = split m{\s}, $indexref;
%index = map {$_ => 1} @indexkeys;
}
return \%index;
}
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lib/Bio/Das/ProServer.pm view on Meta::CPAN
my @coordfull;
while (my $blk = <$fh_coord>) {
$blk =~ s{^\s*(<\?xml.*?>)?(\s*</?DASCOORDINATESYSTEM>\s*)?}{}mixs;
$blk =~ s/\s*$//mxs;
push @coordfull, grep { $_ }
split m{</COORDINATES>}mxs, $blk;
}
close $fh_coord or croak "Unable to close coordinates file $coordfile";
my %coords;
for (@coordfull) {
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lib/Bio/EnsEMBL/Mapper.pm view on Meta::CPAN
Arg 4 int $strand
raw contig orientation (+/- 1)
Arg 5 int $type
nature of transform - gives the type of
coordinates to be transformed *from*
Function inferior map method. Will only do ungapped unsplit mapping.
Will return id, start, end strand in a list.
Returntype list of results
Exceptions none
Caller Bio::EnsEMBL::AssemblyMapper
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lib/Bio/FeatureIO/ptt.pm view on Meta::CPAN
my $self = shift;
$self->mode eq 'r' || return; # returns if can't read next_feature when we're in write mode
my $line = $self->_readline() or return; # returns if end of file, no more features?
chomp $line;
my @col = split m/\t/, $line;
@col==$NUM_COL or $self->throw("Too many columns for PTT line");
$col[0] =~ m/(\d+)\.\.(\d+)/ or $self->throw("Invalid location (column 1)");
my $feat = Bio::SeqFeature::Generic->new(-start=>$1, -end=>$2, -primary=>'CDS');
$col[1] =~ m/^([+-])$/ or $self->throw("Invalid strand (column 2)");
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lib/Bio/GeneDesign/RestrictionEnzymes.pm view on Meta::CPAN
{
my ($path) = @_;
open (my $REFILE, '<', $path) || croak ("Can't read $path!\n");
my $ref = do { local $/ = <$REFILE> };
close $REFILE;
my @list = split m{\s}x, $ref;
return \@list;
}
1;
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lib/Bio/Graphics/FeatureFile.pm view on Meta::CPAN
sub parse_text {
my $self = shift;
my $text = shift;
foreach (split m/\015?\012|\015\012?/,$text) {
$self->parse_line($_);
}
}
sub parse_line {
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lib/Bio/MUST/Apps/OmpaPa/Roles/Parsable.pm view on Meta::CPAN
# use the directory of entry file
my @finalsort;
FINALSORT:
for my $f (@sorted) {
my @parts = split m{/}xms, $f;
if ("$parts[0]/" eq $dir) {
push @finalsort, $f;
next FINALSORT;
}
push @finalsort, $f if @parts < 2;
lib/Bio/MUST/Apps/OmpaPa/Roles/Parsable.pm view on Meta::CPAN
my %count_for;
my %coeffs_for;
for my $hit ($self->all_hits) {
# TODO: use SeqId methods: $_->$method // $_->taxon_id
my $org = (split m{\|}xms, $hit->{acc})[0];
$count_for{$org}++;
my $coeff_len = $hit->{len} / $hit->{qlen};
my $coeff_hmm
= ( $hit->{hmm_to} - $hit->{hmm_from} + 1 ) / $hit->{qlen};
lib/Bio/MUST/Apps/OmpaPa/Roles/Parsable.pm view on Meta::CPAN
sub _org_col {
my $self = shift;
my @ids = map { $_->{acc} } $self->all_hits;
my @orgs = map { (split m{\|}xms, $_)[0] } @ids;
my %count_orgs;
for my $org (@orgs) {
$count_orgs{$org}++;
}
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bin/physeter.pl view on Meta::CPAN
next HIT if $hit->percent_identity < $ARGV_tax_min_ident;
next HIT if $hit->bit_score < $ARGV_tax_min_score;
# fetch hit taxonomy and org
# optimized code (requires taxon_id|accession seq_ids)
my $taxon_id = ( split m{\|}xms, $hit->hit_id )[0];
# k-folds mode (skip hits from current database subset)
next HIT if $ARGV_kfold && $unwanted{$taxon_id};
my @taxonomy = $tax->get_taxonomy($taxon_id);
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lib/Bio/MUST/Core/GeneticCode/Factory.pm view on Meta::CPAN
# get all names and id for current code
my ($id) = $code =~ m/ id \s* (\d+) /xms;
my @names = $code =~ m/ name \s* \"(.*?)\" /xmsg;
@names = map { s{\n}{}xmsgr } @names; # remove newline chars
@names = map { split m{;\s*}xms } @names; # demultiplex names
# retrieve the amino acid line
my ($aa_line) = $code =~ m/ ncbieaa \s* \"(.*?)\" /xms;
$aa_line =~ s{\*}{x}xmsg; # make STOPs MUST-compliant
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lib/Bio/ToolBox/utility.pm view on Meta::CPAN
$c =~ s/IV/4/;
$c =~ s/IX/9/;
$c =~ s/V/5/;
$c =~ s/I/1/g;
my $n = 0;
foreach ( split m//, $c ) {
if ( $_ eq 'X' ) {
$n += 10;
}
else {
$n += $_;
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Bio/DB/Expression/geo.pm view on Meta::CPAN
my $doc = $self->_get_url( URL_PLATFORMS );
$doc =~ s!^.+?>Release date<.+?</tr>(.+)</table>!$1!gs;
my @platforms = ();
my @records = split m!</tr>\s+<tr>!, $doc;
foreach my $record ( @records ) {
my ($platform_acc,$name,$tax_acc,$contact_acc,$contact_name) =
$record =~ m!acc\.cgi\?acc=(.+?)".+?<td.+?>(.+?)<.+?<td.+?>.+?<.+?<td.+?>.+?href=".+?id=(.+?)".+?<td.+?OpenSubmitter\((\d+?)\).+?>(.+?)<!s;
next unless $platform_acc;
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src/boost/serialization/split_member.hpp view on Meta::CPAN
}
} // namespace serialization
} // namespace boost
// split member function serialize funcition into save/load
#define BOOST_SERIALIZATION_SPLIT_MEMBER() \
template<class Archive> \
void serialize( \
Archive &ar, \
const unsigned int file_version \
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include/boost/serialization/split_member.hpp view on Meta::CPAN
}
} // namespace serialization
} // namespace boost
// split member function serialize funcition into save/load
#define BOOST_SERIALIZATION_SPLIT_MEMBER() \
template<class Archive> \
void serialize( \
Archive &ar, \
const unsigned int file_version \
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lib/Bot/BasicBot/Pluggable/Module/MetaSyntactic.pm view on Meta::CPAN
( $command, my @args ) = split /\s+/, $command;
return if !$command || !length $command;
# it's a theme
if ( $command =~ /^[-\w\/]+$/ ) {
my ( $theme, $category ) = split m'/', $command, 2;
$self->{meta}{theme}{$command} //= _load_theme($theme, $category);
return "No such theme: $theme"
if !$META->has_theme($theme);
if ( $category && $self->{meta}{theme}{$command}
->isa('Acme::MetaSyntactic::MultiList')
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lib/Bread/Board/LazyLoader/Obj.pm view on Meta::CPAN
sub _normalize_path {
my ($path) = @_;
return
defined $path
? join( '/', grep { length($_) > 0 } split m{/}, $path )
: '';
}
sub _sub_path {
my ($parent, $name) = @_;
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lib/Bryar/Frontend/Base.pm view on Meta::CPAN
}
sub parse_path {
my ($self, $config) = @_;
my $pi = $self->obtain_path_info();
my @pi = split m{/}, $pi;
shift @pi while @pi and not$pi[0];
#...
my %args;
if ($pi[-1] and $pi[-1] eq "xml") { $args{format} = "xml"; pop @pi; }
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lib/Bubblegum/Object/String.pm view on Meta::CPAN
$string->split(', '); # ['name', 'age', 'dob', 'email']
$string->split(', ', 2); # ['name', 'age, dob, email']
$string->split(qr/\,\s*/); # ['name', 'age', 'dob', 'email']
$string->split(qr/\,\s*/, 2); # ['name', 'age, dob, email']
The split method splits the subject into a list of strings, separating each
chunk by the argument (string or regexp object), and returns that list as an
array reference. This method optionally takes a second argument which would be
the limit (number of matches to capture). Note, this operation expects the 1st
argument to be a Regexp object or a String.
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0.09 2014-12-10 (PERLANCAR)
- No functional changes.
- Use new name of renamed/split module SHARYANTO::String::Util ->
String::Trim::More.
0.08 2014-05-17 (SHARYANTO)
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or die "Cannnot open file $file_name";
local $/ = ();
my $text = <$file>;
# repair last line without \n
$text =~ s{([^\x0D\x0A]) \z}{$1\x0D\x0A}xms;
@lines = split m{\x0A}, $text;
}
my $find_line_numbers = sub {
my ($test_description, $test_reason, $regex, $regex_negation) = @_;
my $line_number = 0;
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bin/fillpdffields.pl view on Meta::CPAN
my $outfile = shift;
if ($opts{background} =~ m/\s/xms)
{
# Separate r,g,b
$opts{background} = [split m/\s+/xms, $opts{background}];
}
my $doc = CAM::PDF->new($infile) || die "$CAM::PDF::errstr\n";
my @list = (@ARGV);
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lib/CAM/PDFTaxforms.pm view on Meta::CPAN
if ($propdict->{Ff})
{
# Just decode the ones we actually care about
# PDF ref, 3rd ed pp 532,543
my $ff = $self->getValue($propdict->{Ff});
my @flags = split m//xms, unpack 'b*', pack 'V', $ff;
$flags{ReadOnly} = $flags[0];
$flags{Required} = $flags[1];
$flags{NoExport} = $flags[2];
$flags{Multiline} = $flags[12];
$flags{Password} = $flags[13];
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local/lib/perl5/Module/Build/Base.pm view on Meta::CPAN
@{ $self->rscan_dir($dir, $self->file_qr("\\.$type\$")) } };
}
sub localize_file_path {
my ($self, $path) = @_;
return File::Spec->catfile( split m{/}, $path );
}
sub localize_dir_path {
my ($self, $path) = @_;
return File::Spec->catdir( split m{/}, $path );
}
sub fix_shebang_line { # Adapted from fixin() in ExtUtils::MM_Unix 1.35
my ($self, @files) = @_;
my $c = ref($self) ? $self->{config} : 'Module::Build::Config';
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}
sub msgs_match {
my ($got, $expected, $message) = @_;
## no critic (RegularExpressions::RequireLineBoundaryMatching)
my ($got_head, $got_body) = split m/\015\012\015\012/xs, $got, 2;
my ($exp_head, $exp_body) = split m/\015\012\015\012/xs, $expected, 2;
my %exp = map {lc($_) => 1} split m/\015\012/xs, $exp_head;
for my $got_head_line (split m/\015\012/xs, $got_head) {
if (!delete $exp{lc $got_head_line}) {
return is($got, $expected, $message . ' -- extra header: ' . $got_head_line); # fail
}
}
if (scalar keys %exp) {
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scripts/generate_index.pl view on Meta::CPAN
=cut
my ($github_user, $github_repo);
if (my $repo = $ENV{GITHUB_REPOSITORY}) {
($github_user, $github_repo) = split m{/}, $repo, 2;
} else {
die 'What repo are you?';
}
my $package_name = $github_repo;
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lib/CGI/Kwiki/Formatter.pm view on Meta::CPAN
}
$_ = $self->lists_format($text);
}
$_;
}
split m!(^[0\*]+ .*?\n)(?=(?:[^0\*]|$))!ms, $text;
}
sub lists_format {
my ($self, $text) = @_;
return $text;
lib/CGI/Kwiki/Formatter.pm view on Meta::CPAN
unless ($switch++ % 2) {
$_ = $self->paragraph_format($_);
}
$_;
}
split m!(\n\s*\n)!ms, $text;
}
sub paragraph_format {
my ($self, $text) = @_;
return '' if $text =~ /^[\s\n]*$/;
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lib/CGI/PathParam.pm view on Meta::CPAN
if ( !$self->path_info ) {
return;
}
return map { $self->unescape($_) }
split m{/}msx, substr $self->path_info, 1;
}
*CGI::path_param = \&path_param;
=head1 DIAGNOSTICS
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CGI/SHTML.pm view on Meta::CPAN
=cut
sub parse_shtml {
my ($self, @lines) = @_;
map { chomp } @lines; my $line = join("\n", @lines);
my @parts = split m/(<!--#.*?-->)/s, $line;
my @return;
while (@parts) {
my @ssi = ();
my $text = shift @parts || "";
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lib/CGI/Snapp.pm view on Meta::CPAN
if ($index && $path_info)
{
$index -= 1 if ($index > 0);
$path_info =~ s!^/!!;
$path_info = (split m|/|, $path_info)[$index] || '';
$mode_source = length $index ? {run_mode => $path_info} : $mode_source;
}
}
$self -> _run_mode_source($mode_source);