package Bio::ASN1::Sequence;
our $AUTHORITY = 'cpan:BIOPERLML';
$Bio::ASN1::Sequence::VERSION = '1.72';
use utf8;
use strict;
use warnings;
use Carp qw(carp croak);
# ABSTRACT: Regular expression-based Perl Parser for ASN.1-formatted NCBI Sequences.
# AUTHOR: Dr. Mingyi Liu <mingyiliu@gmail.com>
# OWNER: 2005 Mingyi Liu
# OWNER: 2005 GPC Biotech AG
# OWNER: 2005 Altana Research Institute
# LICENSE: Perl_5
sub new
{
my $class = shift;
$class = ref($class) if(ref($class));
my $self = { maxerrstr => 20, @_ };
bless $self, $class;
map { $self->input_file($self->{$_}) if($self->{$_}) } qw(file -file);
map { $self->fh($self->{$_}) if($self->{$_}) } qw(fh -fh);
return $self;
}
sub maxerrstr
{
my ($self, $value) = @_;
$self->{maxerrstr} = $value if $value > 0;
return $self->{maxerrstr};
}
sub parse
{
my ($self, $input, $compact, $noreset) = @_;
$input || croak "must have input!\n";
$self->{input} = $input;
$self->{filename} = "input" unless $self->{filename};
$self->{linenumber} = 1 unless $self->{linenumber} && $noreset;
$self->{depth} = 0;
my $result;
eval
{
$result = $self->_parse(); # no need to reset $self->{depth} or linenumber
};
if($@)
{
if($@ !~ /^Data Error:/)
{
croak "non-conforming data broke parser on line $self->{linenumber} in $self->{filename}\n".
"possible cause includes randomly inserted brackets in input file before line $self->{linenumber}\n".
"first $self->{maxerrstr} (or till end of input) characters including the non-conforming data:\n" .
substr($self->{input}, pos($self->{input}), $self->{maxerrstr}) . "\nRaw error mesg: $@\n";
}
else { die $@ }
}
trimdata($result, $compact);
return $result;
}
sub input_file
{
my ($self, $filename) = @_;
# in case user's Perl system can't handle large file. Assuming Unix, otherwise raise error
local *IN; # older styled code to enable module to work with perl 5.005_03
open(*IN, $filename) ||
($! =~ /too large/i && open(*IN, "cat $filename |")) ||
croak "can't open $filename! -- $!\n";
$self->{fh} = *IN;
$self->{filename} = $filename;
$self->{linenumber} = 0; # reset line number
}
sub next_seq
{
my ($self, $compact) = @_;
$self->{fh} || croak "you must pass in a file name or handle through new() or input_file() first before calling next_seq!\n";
local $/ = "Seq-entry ::= set {"; # set record separator
while($_ = readline($self->{fh}))
{
chomp;
next unless /\S/;
my $tmp = (/^\s*Seq-entry ::= set ({.*)/si)? $1 : "{" . $_; # get rid of the 'Seq-entry ::= set ' at the beginning of Sequence record
return $self->parse($tmp, $compact, 1); # 1 species no resetting line number
}
}
sub _parse
{
my ($self, $flag) = @_;
my $data;
while(1)
{
# changing orders of regex if/elsif statements made little difference. current order is close to optimal
if($self->{input} =~ /\G[ \t]*,?[ \t]*\n/cg) # cleanup leftover
{
$self->{linenumber}++;
next;
}
if($self->{input} =~ /\G[ \t]*}/cg)
{
if(!($self->{depth}--) && $self->{input} =~ /\S/)
{
croak "Data Error: extra (mismatched) '}' found on line $self->{linenumber} in $self->{filename}!\n";
}
return $data
}
elsif($self->{input} =~ /\G[ \t]*{/cg)
{
$self->{depth}++;
push(@$data, $self->_parse())
}
elsif($self->{input} =~ /\G[ \t]*([\w-]+)(\s*)/cg)
{
my ($id, $lines) = ($1, $2);
# we're prepared for NCBI to make the format even worse:
# note: to count line numbers right for text files on different OS, I'm sacrificing much speed (maybe I shouldn't worry so much)
$self->{linenumber} += $lines =~ s/\n//g || $lines =~ s/\r//g; # count by *NIX/Win or Mac
my ($tmp, $tmp1);
# we put \s* in lookahead for linenumber counting purpose (which slows things down)
if(($self->{input} =~ /\G"((?:[^"]+|"")*)"(?=\s*[,}])/cg && ++$tmp) ||
($self->{input} =~ /\G'([^']+)'\s*H/icg && ++$tmp1) || # this is the only difference b/w sequence and entrez gene formats so far
$self->{input} =~ /\G([\w-]+)(?=\s*[,}])/cg)
{
my $value = $1;
if($tmp) # slight speed optimization, not really necessary since regex is fast enough
{
$value =~ s/""/"/g;
$self->{linenumber} += $value =~ s/\n//g || $value =~ s/\r//g; # count by *NIX/Win or Mac
$value =~ s/[\r\n]+//g; # in case it's Win format
}
elsif($tmp1) # slight speed optimization, not really necessary since regex is fast enough
{
$value =~ tr/fF8421/NNTGCA/; # good for NCBI4na. But if NCBI8na was used, then more needs to be transliterated
$self->{linenumber} += $value =~ s/\n//g || $value =~ s/\r//g; # count by *NIX/Win or Mac
$value =~ s/[\r\n0]+//g; # in case it's Win format (get rid of '0' at end of seq too)
}
if(ref($data->{$id})) { push(@{$data->{$id}}, $value) } # hash value is not a terminal (or have multiple values), create array to avoid multiple same-keyed hash overwrite each other
elsif($data->{$id}) { $data->{$id} = [$data->{$id}, $value] } # hash value has a second terminal value now!
else { $data->{$id} = $value } # the first terminal value
}
elsif($self->{input} =~ /\G\{/cg)
{
$self->{depth}++;
push(@{$data->{$id}}, $self->_parse());
}
elsif($self->{input} =~ /\G(?=[,}])/cg) { push(@$data, $id) }
else # must be "id value value" format
{
$self->{depth}++;
push(@{$data->{$id}}, $self->_parse(1))
}
if($flag)
{
if(!($self->{depth}--) && $self->{input} =~ /\S/)
{
croak "Data Error: extra (mismatched) '}' found on line $self->{linenumber} in $self->{filename}!\n";
}
return $data;
}
}
elsif($self->{input} =~ /\G[ \t]*"((?:[^"]+|"")*)"(?=\s*[,}])/cg)
{
my $value = $1;
$value =~ s/""/"/g;
$self->{linenumber} += $value =~ s/\n//g || $value =~ s/\r//g; # count by *NIX/Win or Mac
$value =~ s/[\r\n]+//g; # in case it's Win format
push(@$data, $value)
}
else # end of input
{
my ($pos, $len) = (pos($self->{input}), length($self->{input}));
if($pos != $len && $self->{input} =~ /\G\s*\S/cg) # problem with parsing, must be non-conforming data
{
croak "Data Error: none conforming data found on line $self->{linenumber} in $self->{filename}!\n" .
"first $self->{maxerrstr} (or till end of input) characters including the non-conforming data:\n" .
substr($self->{input}, $pos, $self->{maxerrstr}) . "\n";
}
elsif($self->{depth} > 0)
{
croak "Data Error: missing '}' found at end of input in $self->{filename}!";
}
elsif($self->{depth} < 0)
{
croak "Data Error: extra (mismatched) '}' found at end of input in $self->{filename}!";
}
return $data;
}
}
}
# following copied directly from my Pipeline::Util::util just to make this module
# more self-sufficient. Changes should be made over in that module though.
# trims arrayrefs that points to one-element array to slims the
# data structure down (calls Pipeline::Util::util::trimdata)
# something like
# 'comments' => ARRAY(0x898be94)
# 0 ARRAY(0x883fc54)
# 0 ARRAY(0x886aef4)
# 0 HASH(0x884d554)
# 'heading' => 'LocusTagLink'
# 'source' => ARRAY(0x8810714)
# 0 ARRAY(0x8a7df18)
# 0 ARRAY(0x889f940)
# 0 HASH(0x886ada4)
# 'src' => ARRAY(0x88454fc)
# 0 ARRAY(0x8845598)
# 0 HASH(0x898c0ec)
# 'db' => 'HGNC'
# 'tag' => ARRAY(0x898bfb4)
# 0 HASH(0x898c164)
# 'id' => 5
# becomes this if $flag == 1:
# 'comments' => ARRAY(0x8840014)
# 0 HASH(0x884d8a4)
# 'heading' => 'LocusTagLink'
# 'source' => HASH(0x8a9869c)
# 'src' => HASH(0x884534c)
# 'db' => 'HGNC'
# 'tag' => HASH(0x88453c4)
# 'id' => 5
# so now $hash->{comments}->[0]->[0]->[0]->{source}->[0]->[0]->[0]->{src}->[0]->[0]->{tag}->[0]->{id}
# becomes $hash->{comments}->[0]->{source}->{src}->{tag}->{id}
# this may create problem as array might suddenly change to hash depending on whether it
# has multiple elements or not. So set $flag to 2 or 0/undef would disallow trimming that
# would lead to data type change, thus resulting in data structure like:
# 'comments' => ARRAY(0x88617e8)
# 0 HASH(0x889d578)
# 'heading' => 'LocusTagLink'
# 'source' => ARRAY(0x8912244)
# 0 HASH(0x8a5d648)
# 'src' => ARRAY(0x8a2203c)
# 0 HASH(0x8a1af10)
# 'db' => 'HGNC'
# 'tag' => ARRAY(0x8a1add8)
# 0 HASH(0x8a1af88)
# 'id' => 5
# still not the safest, but saves some hassle writing code
sub trimdata
{
my ($ref, $flag) = @_;
$flag = 2 unless $flag;
return if $flag == 3 || !ref($ref);
if(ref($ref) ne 'ARRAY') # allows for object refs
{
my @keys;
eval { @keys = keys %$ref }; # let's be careful and check if it can work as a hash
return if $@;
foreach my $key (@keys)
{
my $tmp = $ref->{$key};
while(ref($tmp) eq 'ARRAY' && @$tmp == 1)
{
last if($flag == 2 && ref($tmp->[0]) ne 'ARRAY');
$tmp = $tmp->[0]
}
$ref->{$key} = $tmp;
trimdata($ref->{$key}, $flag) if(ref($ref->{$key}))
}
}
else
{
# since the only situations where we would get an array of array is
# when ASN file has a bracket of brackets (otherwise we'd get at least
# a hash), it makes sense to reduce the arrayrefs to one level
foreach my $item (@$ref)
{
my $tmp = $item;
while(ref($tmp) eq 'ARRAY' && @$tmp == 1)
{
$tmp = $tmp->[0];
}
$item = $tmp;
trimdata($item, $flag) if(ref($item))
}
}
}
sub fh
{
my ($self, $filehandle) = @_;
if($filehandle)
{
$self->{fh} = $filehandle;
$self->{linenumber} = 0; # reset line number
}
return $self->{fh};
}
sub rawdata
{
my $self = shift;
return "Seq-entry ::= set $self->{input}";
}
1;
__END__
=pod
=encoding utf-8
=head1 NAME
Bio::ASN1::Sequence - Regular expression-based Perl Parser for ASN.1-formatted NCBI Sequences.
=head1 VERSION
version 1.72
=head1 SYNOPSIS
use Bio::ASN1::Sequence;
my $parser = Bio::ASN1::Sequence->new('file' => "downloaded.asn1");
while(my $result = $parser->next_seq)
{
# extract data from $result, or Dumpvalue->new->dumpValue($result);
}
# a new way to get the $result data hash for a particular sequence id:
use Bio::ASN1::Sequence::Indexer;
my $inx = Bio::ASN1::Sequence::Indexer->new(-filename => 'seq.idx');
my $seq = $inx->fetch_hash('AF093062');
# for creation of .idx index files please refer to
# Bio::ASN1::Sequence::Indexer perldoc
=head1 DESCRIPTION
Bio::ASN1::Sequence is a regular expression-based Perl Parser for ASN.1-formatted
NCBI sequences. It parses an ASN.1-formatted sequence record and returns a data
structure that contains all data items from the sequence record.
The parser will report error & line number if input data does not conform to the
NCBI Sequence annotation file format.
The sequence parser is basically a modified version of the high-performance
Bio::ASN1::EntrezGene parser. However, I created a standalone module for sequence
since it is more efficient to keep Sequence-specific code out of EntrezGene.pm.
In fact it is possible to provide reading of all NCBI's ASN.1-formatted
files through simple variations of the Entrez Gene parser (I need more
investigation to be sure, but at least the sequence parser works well).
Since demand for parsing NCBI ASN.1-formatted sequences is much lower than EntrezGene,
this module is more like a beta version that works on the examples I checked, but
I did not check all available records or data definitions. The error-reporting
function of this module has to be useful sometimes. :)
=head1 ATTRIBUTES
=head2 maxerrstr
Parameters: $maxerrstr (optional) - maximum number of characters after
offending element, used by error reporting, default is 20
Example: $parser->maxerrstr(20);
Function: get/set maxerrstr.
Returns: maxerrstr.
Notes:
=head2 input_file
Parameters: $filename for file that contains Sequence record(s)
Example: $parser->input_file($filename);
Function: Takes in name of a file containing Sequence records.
opens the file and stores file handle
Returns: none.
Notes: Attempts to open file larger than 2 GB even on Perl that
does not support 2 GB file (accomplished by calling
"cat" and piping output. On OS that does not have "cat"
error message will be displayed)
=head1 METHODS
=head2 new
Parameters: maxerrstr => 20 (optional) - maximum number of characters after
offending element, used by error reporting, default is 20
file or -file => $filename (optional) - name of the file to be
parsed. call next_seq to parse!
fh or -fh => $filehandle (optional) - handle of the file to be
parsed.
Example: my $parser = Bio::ASN1::Sequence->new();
Function: Instantiate a parser object
Returns: Object reference
Notes: Setting file or fh will reset line numbers etc. that are used
for error reporting purposes, and seeking on file handle would
mess up linenumbers!
=head2 parse
Parameters: $string that contains Sequence record,
$trimopt (optional) that specifies how the data structure
returned should be trimmed. 2 is recommended and
default
$noreset (optional) that species that line number should not
be reset
DEPRECATED as external function!!! Do not call this function
directly! Call next_seq() instead
Example: my $value = $parser->parse($text); # DEPRECATED as
# external function!!! Do not call this function
# directly! Call next_seq() instead
Function: Takes in a string representing Sequence record, parses
the record and returns a data structure.
Returns: A data structure containing all data items from the sequence
record.
Notes: DEPRECATED as external function!!! Do not call this function
directly! Call next_seq() instead
$string should not contain 'Seq-entry ::= set' at beginning!
=head2 next_seq
Parameters: $trimopt (optional) that specifies how the data structure
returned should be trimmed. option 2 is recommended and
default
Example: my $value = $parser->next_seq();
Function: Use the file handle generated by input_file, parses the next
the record and returns a data structure.
Returns: A data structure containing all data items from the sequence
record.
Notes: Must pass in a filename through new() or input_file() first!
For details on how to use the $trimopt data trimming option
please see comment for the trimdata method. An option
of 2 is recommended and default
The acceptable values for $trimopt include:
1 - trim as much as possibile
2 (or 0, undef) - trim to an easy-to-use structure
3 - no trimming (in version 1.06, prior to version
1.06, 0 or undef means no trimming)
=head2 trimdata
Parameters: $hashref or $arrayref
$trimflag (optional, see Notes)
Example: trimdata($datahash); # using the default flag
Function: recursively process all attributes of a hash/array
hybrid and get rid of any arrayref that points to
one-element arrays (trims data structure) depending on
the optional flag.
Returns: none - trimming happenes in-place
Notes: This function is useful to compact a data structure produced by
Bio::ASN1::Sequence::parse.
The acceptable values for $trimopt include:
1 - trim as much as possibile
2 (or 0, undef) - trim to an easy-to-use structure
3 - no trimming (in version 1.06, prior to version
1.06, 0 or undef means no trimming)
This function is duplicate to EntrezGene.pm's and code should
be compressed in the future (using util module & subclass).
=head2 fh
Parameters: $filehandle (optional)
Example: trimdata($datahash); # using the default flag
Function: getter/setter for file handle
Returns: file handle for current file being parsed.
Notes: Use with care!
Line number report would not be corresponding to file's line
number if seek operation is performed on the file handle!
=head2 rawdata
Parameters: none
Example: my $data = $parser->rawdata();
Function: Get the sequence data file that was just parsed
Returns: a string containing the ASN1-formatted sequence record
Notes: Must first parse a record then call this function!
Could be useful in interpreting line number value in error
report (if user did a seek on file handle right before parsing
call)
=head1 INTERNAL METHODS
=head2 _parse
NCBI's Apr 05, 2005 format change forced much usage of lookahead, which would for
sure slows parser down. But can't code efficiently without it.
=head1 PREREQUISITE
None.
=head1 INSTALLATION
Bio::ASN1::Sequence is part of the Bio::ASN1::EntrezGene package.
Bio::ASN1::EntrezGene package can be installed & tested as follows:
perl Makefile.PL
make
make test
make install
=head1 SEE ALSO
The parse_sequence_example.pl script included in this package (please
see the Bio-ASN1-EntrezGene-x.xx/examples directory) shows the usage.
Please check out perldoc for Bio::ASN1::EntrezGene for more info.
=head1 CITATION
Liu, Mingyi, and Andrei Grigoriev. "Fast parsers for Entrez Gene."
Bioinformatics 21, no. 14 (2005): 3189-3190.
=head1 OPERATION SYSTEMS SUPPORTED
Any OS that Perl runs on.
=head1 FEEDBACK
=head2 Mailing lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Dr. Mingyi Liu <mingyiliu@gmail.com>
=head1 COPYRIGHT
This software is copyright (c) 2005 by Mingyi Liu, 2005 by GPC Biotech AG, and 2005 by Altana Research Institute.
This software is available under the same terms as the perl 5 programming language system itself.
=cut