App-Sandy
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lib/App/Sandy/DB/Handle/Expression.pm view on Meta::CPAN
package App::Sandy::DB::Handle::Expression;
# ABSTRACT: Class to handle expression-matrix database schemas.
use App::Sandy::Base 'class';
use App::Sandy::DB;
use IO::Compress::Gzip 'gzip';
use IO::Uncompress::Gunzip 'gunzip';
use Storable qw/nfreeze thaw/;
use Scalar::Util 'looks_like_number';
with 'App::Sandy::Role::IO';
our $VERSION = '0.25'; # VERSION
sub insertdb {
my ($self, $file, $name, $source, $is_user_provided) = @_;
my $schema = App::Sandy::DB->schema;
log_msg ":: Checking if there is already an expression-matrix '$name' ...";
lib/App/Sandy/DB/Handle/Expression.pm view on Meta::CPAN
chomp;
next if /^\s*$/;
my @fields = split;
die "Error parsing expression-matrix '$file': Seqid (first column) not found at line $line\n"
unless defined $fields[0];
die "Error parsing expression-matrix '$file': Count (second column) not found at line $line\n"
unless defined $fields[1];
die "Error parsing expression-matrix '$file': Count (second column) does not look like a number at line $line\n"
if not looks_like_number($fields[1]);
# Only throws a warning, because it is common zero values in expression matrix
if ($fields[1] <= 0) {
log_msg ":: Parsing expression-matrix '$file': Ignoring seqid '$fields[0]': Count (second column) lesser or equal to zero at line $line\n";
next;
}
$indexed_file{$fields[0]} = $fields[1];
}
lib/App/Sandy/DB/Handle/Variation.pm view on Meta::CPAN
package App::Sandy::DB::Handle::Variation;
# ABSTRACT: Class to handle structural variation database schemas.
use App::Sandy::Base 'class';
use App::Sandy::DB;
use IO::Compress::Gzip 'gzip';
use IO::Uncompress::Gunzip 'gunzip';
use Storable qw/nfreeze thaw/;
use Scalar::Util qw/looks_like_number refaddr/;
use List::Util 'max';
with qw/App::Sandy::Role::IO App::Sandy::Role::SeqID/;
our $VERSION = '0.25'; # VERSION
sub insertdb {
my ($self, $file, $name, $source, $is_user_provided, $type, @args) = @_;
my $schema = App::Sandy::DB->schema;
lib/App/Sandy/DB/Handle/Variation.pm view on Meta::CPAN
next if /^#/;
next if /^\s*$/;
chomp;
my @fields = split;
die "Not found all fields (SEQID, POSITION, ID, REFERENCE, OBSERVED, GENOTYPE) into file '$variation_file' at line $line\n"
unless scalar @fields >= 6;
die "Second column, position, does not seem to be a number into file '$variation_file' at line $line\n"
unless looks_like_number($fields[1]);
die "Second column, position, has a value lesser or equal to zero into file '$variation_file' at line $line\n"
if $fields[1] <= 0;
die "Fourth column, reference, does not seem to be a valid entry: '$fields[3]' into file '$variation_file' at line $line\n"
unless $fields[3] =~ /^(\w+|-)$/;
die "Fifth column, alteration, does not seem to be a valid entry: '$fields[4]' into file '$variation_file' at line $line\n"
unless $fields[4] =~ /^(\w+|-)$/;
lib/App/Sandy/DB/Handle/Variation.pm view on Meta::CPAN
}
unless ($has_header) {
die "No header found in file '$vcf_file'\n";
}
die "Not found all columns into file '$vcf_file' at line $line\n"
unless scalar @fields > 9;
die "Second column, position, does not seem to be a number into file '$vcf_file' at line $line\n"
unless looks_like_number($fields[1]);
die "Second column, position, has a value lesser or equal to zero into file '$vcf_file' at line $line\n"
if $fields[1] <= 0;
die "Fourth column, reference, does not seem to be a valid entry: '$fields[3]' into file '$vcf_file' at line $line\n"
unless $fields[3] =~ /^(<\w+(:\w+)*>|\w+|-)$/;
die "Fifth column, alternate, does not seem to be a valid entry: '$fields[4]' into file '$vcf_file' at line $line\n"
unless $fields[4] =~ /^(\w+|<\w+(:\w+)*>|-|\*)(,(\w+|<\w+(:\w+)*>|-|\*))*$/;
}
usage() if $opt{help};
strip() if $opt{strip};
$opt{'compat-version'} = 5.003_07 unless exists $opt{'compat-version'};
$opt{'compat-version'} = int_parse_version($opt{'compat-version'});
my $int_min_perl = int_parse_version(5.003_07);
# Each element of this hash looks something like:
# 'Poison' => {
# 'base' => '5.008000',
# 'provided' => 1,
# 'todo' => '5.003007'
# },
my %API = map { /^(\w+)\|([^|]*)\|([^|]*)\|(\w*)$/
? ( $1 => {
($2 ? ( base => $2 ) : ()),
($3 ? ( todo => $3 ) : ()),
(index($4, 'v') >= 0 ? ( varargs => 1 ) : ()),
LONGJMP_tb_pb|5.033003||Viu
LONGLONGSIZE|5.005000|5.005000|Vn
LONGSIZE|5.004000|5.003007|oVn
LOOKBEHIND_END_t8_p8|||Viu
LOOKBEHIND_END_t8_pb|||Viu
LOOKBEHIND_END_t8|||Viu
LOOKBEHIND_END_tb_p8|||Viu
LOOKBEHIND_END_tb_pb|||Viu
LOOKBEHIND_END_tb|||Viu
LOOKBEHIND_END|||Viu
looks_like_bool|5.027008||Viu
looks_like_number|5.003007|5.003007|
LOOP_PAT_MODS|5.009005||Viu
lop|5.005000||Viu
lossless_NV_to_IV|5.031001||Vniu
LOWEST_ANYOF_HRx_BYTE|5.031002||Viu
L_R_TZSET|5.009005|5.009005|Vn
lsbit_pos32|5.035003||cVnu
lsbit_pos|5.035004||Viu
lsbit_pos64|5.035003||cVnu
lsbit_pos_uintmax|5.035003||Viu
lseek|5.005000||Viu
# define D_PPP_TO_FOLD_CALLEE(s,r,l) \
Perl__to_utf8_fold_flags(aTHX_ s, r, l, FOLD_FLAGS_FULL, NULL)
# endif
/* The actual implementation of the backported macros. If too short, croak,
* otherwise call the original that doesn't have an upper limit parameter */
# define D_PPP_GENERIC_MULTI_ARG_TO(name, s, e,r,l) \
(((((e) - (s)) <= 0) \
/* We could just do nothing, but modern perls croak */ \
? (croak("Attempting case change on zero length string"), \
0) /* So looks like it returns something, and will compile */ \
: ((e) - (s)) < UTF8SKIP(s)) \
? (croak(D_PPP_TOO_SHORT_MSG, \
s[0], (int) ((e) - (s)), (int) UTF8SKIP(s)), \
0) \
: D_PPP_TO_ ## name ## _CALLEE(s,r,l))
#ifndef toUPPER_utf8_safe
# define toUPPER_utf8_safe(s,e,r,l) \
D_PPP_GENERIC_MULTI_ARG_TO(UPPER,s,e,r,l)
#endif
D_PPP_GENERIC_SINGLE_ARG_TO_UVCHR(title, c, s, l)
#endif
#ifndef toFOLD_uvchr
# define toFOLD_uvchr(c, s, l) toLOWER_uvchr(c, s, l)
#endif
# define D_PPP_GENERIC_SINGLE_ARG_TO_UTF8(name, s, e, r, l) \
(((((e) - (s)) <= 0) \
? (croak("Attempting case change on zero length string"), \
0) /* So looks like it returns something, and will compile */ \
: ((e) - (s)) < UTF8SKIP(s)) \
? (croak(D_PPP_TOO_SHORT_MSG, \
s[0], (int) ((e) - (s)), (int) UTF8SKIP(s)), \
0) \
/* Get the changed code point and store its UTF-8 */ \
: D_PPP_UV_TO_UTF8(r, to_utf8_ ## name(s)), \
/* Then store its length, and re-get code point for return */ \
*(l) = UTF8SKIP(r), to_utf8_ ## name(r))
/* Warning: toUPPER_utf8_safe, toLOWER_utf8_safe, toTITLE_utf8_safe,
( run in 0.392 second using v1.01-cache-2.11-cpan-64827b87656 )