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Updated trunk to 0.5.2
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git-svn-id: https://jcvi-tools.svn.sourceforge.net/svnroot/jcvi-tools/JCVI-Translator/trunk@18 a16988d2-67c9-4db9-a897-0603be59747b
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kgalinsky committed Oct 28, 2009
1 parent 28769aa commit d4b7986
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Showing 3 changed files with 98 additions and 57 deletions.
4 changes: 4 additions & 0 deletions Changes
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Original file line number Diff line number Diff line change
@@ -1,5 +1,9 @@
Revision history for JCVI-Translator

0.5.2 Apr 13 2009
- Even more documentation in Utils
- codons/regex/find method in Utils can take "stop" for stop codons

0.5.1 Apr 13 2009
- Better documentation in Utils
- Fixed bugs in JCVI::Translator::Utils::regex and find
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2 changes: 1 addition & 1 deletion lib/JCVI/Translator.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ use strict;
use warnings;

use version;
our $VERSION = qv('0.5.1');
our $VERSION = qv('0.5.2');

use base qw(Class::Accessor::Fast);
__PACKAGE__->mk_accessors(qw(table base));
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149 changes: 93 additions & 56 deletions lib/JCVI/Translator/Utils.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -47,10 +47,19 @@ use Params::Validate;
use JCVI::DNATools qw( cleanDNA );
use JCVI::AATools qw( $aa_match );

# Default values
our $DEFAULT_STRAND = 1;
our $DEFAULT_SEARCH_STRAND = 0;
our $DEFAULT_SANITIZED = 0;

# Precompiled regular expressions for SPOT rule and to save time
our $BOOLEAN_REGEX = qr/^[01]$/;
our $INTEGER_REGEX = qr/^\d+$/;
our $STRAND_REGEX = qr/^[+-]?1$/;
our $SEARCH_STRAND_REGEX = qr/^[+-]?[01]$/;
our $RESIDUE_REGEX = qr/^(?:$aa_match|start|stop|lower|upper)$/;
our $STRICT_REGEX = qr/^[012]$/;

sub _new {
my $self = shift->SUPER::_new(@_);
$self->_regexes( [ {}, {} ] );
Expand All @@ -66,9 +75,18 @@ sub _new {
my $codon_array = $translator->codons( $residue);
my $codon_array = $translator->codons( $residue, \%params );
Returns a list of codons for a particular residue or start codon. For start
codons, input "start" for the residue. Valid options for the params
hash are:
Returns a list of codons for a particular residue or start codon. In addition
to the one-letter codes for amino acids, the following are valid inputs for the
residue:
start: Start codons
stop: Stop codons (you may also use "*" which is the 1 letter code)
lower: Start or stop codons, depending up on strand
upper: Start or stop codons, depending up on strand
"lower" and "upper" match the respective ends of a CDS for a given strand (i.e.
on the positive strand, lower matches the start, and upper matches them stop).
Valid options for the params hash are:
strand: 1 or -1; default = 1
Expand All @@ -85,36 +103,39 @@ sub codons {
@_,
{
type => Params::Validate::SCALAR,
regex => qr/^(?:$aa_match|start|lower|upper)$/
regex => $RESIDUE_REGEX
},
{ type => Params::Validate::HASHREF, default => {} }
);

my %p = validate(
@p,
{

# Make sure strand is 1 or -1 and set default
strand => {
default => $DEFAULT_STRAND,
regex => qr/^[+-]?1$/,
regex => $STRAND_REGEX,
type => Params::Validate::SCALAR
}

}
);

# Set the reverse comlement variable
my $rc = $p{strand} == 1 ? 0 : 1;

# If residue is 'stop' change it to '*'
if ( $residue eq 'stop' ) { $residue = '*' }

# Do nothing if residue is "start" (don't want to capitalize)
elsif ( $residue eq 'start' ) { }

# Lower bound is "*" on the - strand, "start" on the + strand
if ( $residue eq 'lower' ) { $residue = $rc ? '*' : 'start' }
elsif ( $residue eq 'lower' ) { $residue = $rc ? '*' : 'start' }

# Upper bound is "start" on the - strand, or "*" on the + strand
elsif ( $residue eq 'upper' ) { $residue = $rc ? 'start' : '*' }

# Do nothing if residue is "start" (don't want to capitalize)
elsif ( $residue eq 'start' ) { }

# Capitalize all other residues
else { $residue = uc $residue }

Expand All @@ -133,18 +154,19 @@ sub codons {
my $regex = $translator->regex( $residue, \%params );
Returns a regular expression matching codons for a particular amino acid
residue. In addition, three special values are allowed:
residue. In addition to the one-letter codes for amino acids, the following are
valid inputs for the residue:
start: Start codons
stop: Stop codons (you may also use "*" which is the 1 letter code)
lower: Start or stop codons, depending up on strand
lower: Start or stop codons, depending up on strand
upper: Start or stop codons, depending up on strand
lower and upper match the respective ends of a CDS for a given strand (i.e. on
the positive strand, lower matches the start, and upper matches the stop). The
stop codon is stored as "*" by the translator. Valid options for the params
hash are:
"lower" and "upper" match the respective ends of a CDS for a given strand (i.e.
on the positive strand, lower matches the start, and upper matches the stop).
Valid options for the params hash are:
strand: 1 or -1; default = 1
strand: 1 or -1; default = 1
=cut

Expand All @@ -156,16 +178,14 @@ sub regex {

( $residue, $p[0] ) = validate_pos(
@_,
{
type => Params::Validate::SCALAR,
regex => qr/^(?:$aa_match|start|lower|upper)$/
},
{ type => Params::Validate::SCALAR },
{ type => Params::Validate::HASHREF, default => {} }
);

my %p = validate(
@p,
{

# Make sure strand is 1 or -1 and set default
strand => {
default => $DEFAULT_STRAND,
Expand All @@ -186,12 +206,13 @@ sub regex {
}

# If the regex wasn't defined, build it by calling codons
$regex = join '|', @{ $self->codons(@_) };
$regex = join '|', @{ $self->codons( $residue, \%p ) };
$regex = qr/$regex/;

# Cache the regex and return it
$self->_regexes->[$rc]->{$residue} = $regex;
TRACE 'caching regular expression, leaving regex';

TRACE 'cached regular expression, leaving regex';
return $regex;
}

Expand All @@ -200,8 +221,18 @@ sub regex {
my $locations = $translator->find( $seq_ref, $residue );
my $locations = $translator->find( $seq_ref, $residue, \%params );
Find the indexes of a given residue in a sequence. Valid options for the params
hash are:
Find the indexes of a given residue in a sequence. In addition to the
one-letter codes for amino acids, the following are valid inputs for the
residue:
start: Start codons
stop: Stop codons (you may also use "*" which is the 1 letter code)
lower: Start or stop codons, depending up on strand
upper: Start or stop codons, depending up on strand
"lower" and "upper" match the respective ends of a CDS for a given strand (i.e.
on the positive strand, lower matches the start, and upper matches the stop).
Valid options for the params hash are:
strand: 1 or -1; default = 1
Expand All @@ -214,23 +245,32 @@ sub find {
my ( $seq_ref, $residue, @p );

( $seq_ref, $residue, $p[0] ) = validate_pos(
@_, { type => Params::Validate::SCALARREF },
1, { default => {}, type => Params::Validate::HASHREF }
);

my %p = validate(
@p,
{
strand => {
default => $DEFAULT_STRAND,
regex => qr/^[+-]?1$/,
type => Params::Validate::SCALAR
}
}
@_,
{ type => Params::Validate::SCALARREF },
{ type => Params::Validate::SCALAR },
{ default => {}, type => Params::Validate::HASHREF }
);

my $regex = $self->regex( $residue, \%p );

# Strand is unnecessary for now. Uncomment this section when other options
# are added to find.
# my %p = validate(
# @p,
# {
# strand => {
# default => $DEFAULT_STRAND,
# regex => $STRAND_REGEX,
# type => Params::Validate::SCALAR
# }
# }
# );
#
# my $regex = $self->regex( $residue, \%p );

my $regex = $self->regex( $residue, $p[0] );

# Use a look-ahead in the regular expression. For instance, if the amino
# acid has the codon AAA, and you have a poly-A region, the match will be
# at every single base, not every 3 bases.
my @positions;
while ( $$seq_ref =~ m/(?=$regex)/ig ) {
push @positions, pos($$seq_ref);
Expand Down Expand Up @@ -273,16 +313,14 @@ You can also specify which strand you are looking for the ORF to be on.
For ORFs starting at the very beginning of the strand or trailing off the end,
but not in phase with the start or ends, this method will cut at the last
complete codon.
Eg:
complete codon. For example, if the following was the longest ORF:
0 1 2 3 4 5 6 7 8 9 10
A C G T A G T T T A
*****
<--------------->
Will return:
getORF will return:
{
strand => 1,
Expand Down Expand Up @@ -327,14 +365,14 @@ sub getORF {
# Verify that strand is -1, 0 or 1, set default
strand => {
default => $DEFAULT_SEARCH_STRAND,
regex => qr/^[+-]?[01]$/,
regex => $SEARCH_STRAND_REGEX,
type => Params::Validate::SCALAR
},

# Verify that lower is within the sequence, default to 0
lower => {
default => 0,
regex => qr/^[0-9]+$/,
regex => $INTEGER_REGEX,
type => Params::Validate::SCALAR,
callbacks => {
'lower >= 0' => sub { $_[0] >= 0 },
Expand All @@ -345,7 +383,7 @@ sub getORF {
# Verify that upper is within the sequence, default to length
upper => {
default => length($$seq_ref),
regex => qr/^[0-9]+$/,
regex => $INTEGER_REGEX,
type => Params::Validate::SCALAR,
callbacks => {
'upper >= 0' => sub { $_[0] >= 0 },
Expand All @@ -356,7 +394,7 @@ sub getORF {
# Verify that sanitized is a boolean, set default
sanitized => {
default => $DEFAULT_SANITIZED,
regex => qr/^[01]$/,
regex => $BOOLEAN_REGEX,
type => Params::Validate::SCALAR
}
}
Expand Down Expand Up @@ -503,14 +541,14 @@ sub getCDS {
# Verify that strand is -1, 0 or 1, set default
strand => {
default => $DEFAULT_SEARCH_STRAND,
regex => qr/^[+-]?[01]$/,
regex => $SEARCH_STRAND_REGEX,
type => Params::Validate::SCALAR
},

# Verify that lower is within the sequence, default to 0
lower => {
default => 0,
regex => qr/^[0-9]+$/,
regex => $INTEGER_REGEX,
type => Params::Validate::SCALAR,
callbacks => {
'lower >= 0' => sub { $_[0] >= 0 },
Expand All @@ -521,7 +559,7 @@ sub getCDS {
# Verify that upper is within the sequence, default to length
upper => {
default => length($$seq_ref),
regex => qr/^[0-9]+$/,
regex => $INTEGER_REGEX,
type => Params::Validate::SCALAR,
callbacks => {
'upper >= 0' => sub { $_[0] >= 0 },
Expand All @@ -532,14 +570,13 @@ sub getCDS {
# Verify that strict is 0, 1 or 2, default to 1
strict => {
default => 1,
regex => qr/^[012]$/,

regex => $STRICT_REGEX,
},

# Verify that sanitized is a boolean, set default
sanitized => {
default => $DEFAULT_SANITIZED,
regex => qr/^[01]$/,
regex => $BOOLEAN_REGEX,
type => Params::Validate::SCALAR
}
}
Expand Down Expand Up @@ -724,14 +761,14 @@ sub nonstop {
# Verify that strand is -1, 0 or 1, default to 0
strand => {
default => $DEFAULT_SEARCH_STRAND,
regex => qr/^[+-]?[01]$/,
regex => $SEARCH_STRAND_REGEX,
type => Params::Validate::SCALAR
},

# Verify that sanitized is a boolean, set default
sanitized => {
default => $DEFAULT_SANITIZED,
regex => qr/^[01]$/,
regex => $BOOLEAN_REGEX,
type => Params::Validate::SCALAR
}
}
Expand Down

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