#
# BioPerl module for Bio::Perl
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Ewan Birney <birney@ebi.ac.uk>
#
# Copyright Ewan Birney
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Perl - Functional access to BioPerl for people who don't know objects
=head1 SYNOPSIS
use Bio::Perl;
# will guess file format from extension
$seq_object = read_sequence($filename);
# forces genbank format
$seq_object = read_sequence($filename,'genbank');
# reads an array of sequences
@seq_object_array = read_all_sequences($filename,'fasta');
# sequences are Bio::Seq objects, so the following methods work
# for more info see Bio::Seq, or do 'perldoc Bio/Seq.pm'
print "Sequence name is ",$seq_object->display_id,"\n";
print "Sequence acc is ",$seq_object->accession_number,"\n";
print "First 5 bases is ",$seq_object->subseq(1,5),"\n";
# get the whole sequence as a single string
$sequence_as_a_string = $seq_object->seq();
# writing sequences
write_sequence(">$filename",'genbank',$seq_object);
write_sequence(">$filename",'genbank',@seq_object_array);
# making a new sequence from just a string
$seq_object = new_sequence("ATTGGTTTGGGGACCCAATTTGTGTGTTATATGTA",
"myname","AL12232");
# getting a sequence from a database (assumes internet connection)
$seq_object = get_sequence('swissprot',"ROA1_HUMAN");
$seq_object = get_sequence('embl',"AI129902");
$seq_object = get_sequence('genbank',"AI129902");
# BLAST a sequence (assumes an internet connection)
$blast_report = blast_sequence($seq_object);
write_blast(">blast.out",$blast_report);
=head1 DESCRIPTION
Easy first time access to BioPerl via functions.
=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 one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org
=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
the bugs and their resolution. Bug reports can be submitted via the web:
https://github.com/bioperl/bioperl-live/issues
=head1 AUTHOR - Ewan Birney
Email birney@ebi.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
#'
# Let the code begin...
package Bio::Perl;
use vars qw(@EXPORT @EXPORT_OK $DBOKAY);
use strict;
use Carp;
use Bio::SeqIO;
use Bio::Seq;
use Bio::Root::Version '$VERSION';
BEGIN {
eval {
require Bio::DB::EMBL;
require Bio::DB::GenBank;
require Bio::DB::SwissProt;
require Bio::DB::RefSeq;
require Bio::DB::GenPept;
};
if( $@ ) {
$DBOKAY = 0;
} else {
$DBOKAY = 1;
}
}
use base qw(Exporter);
@EXPORT = qw(read_sequence read_all_sequences write_sequence
new_sequence get_sequence translate translate_as_string
reverse_complement revcom revcom_as_string
reverse_complement_as_string blast_sequence write_blast);
@EXPORT_OK = @EXPORT;
=head2 read_sequence
Title : read_sequence
Usage : $seq = read_sequence('sequences.fa')
$seq = read_sequence($filename,'genbank');
# pipes are fine
$seq = read_sequence("my_fetching_program $id |",'fasta');
Function: Reads the top sequence from the file. If no format is given, it will
try to guess the format from the filename. If a format is given, it
forces that format. The filename can be any valid perl open() string
- in particular, you can put in pipes
Returns : A Bio::Seq object. A quick synopsis:
$seq_object->display_id - name of the sequence
$seq_object->seq - sequence as a string
Args : Two strings, first the filename - any Perl open() string is ok
Second string is the format, which is optional
For more information on Seq objects see L<Bio::Seq>.
=cut
sub read_sequence{
my ($filename,$format) = @_;
if( !defined $filename ) {
confess "read_sequence($filename) - usage incorrect";
}
my $seqio;
if( defined $format ) {
$seqio = Bio::SeqIO->new( '-file' => $filename, '-format' => $format);
} else {
$seqio = Bio::SeqIO->new( '-file' => $filename);
}
my $seq = $seqio->next_seq();
return $seq;
}
=head2 read_all_sequences
Title : read_all_sequences
Usage : @seq_object_array = read_all_sequences($filename);
@seq_object_array = read_all_sequences($filename,'genbank');
Function: Just as the function above, but reads all the sequences in the
file and loads them into an array.
For very large files, you will run out of memory. When this
happens, you've got to use the SeqIO system directly (this is
not so hard! Don't worry about it!).
Returns : array of Bio::Seq objects
Args : two strings, first the filename (any open() string is ok)
second the format (which is optional)
See L<Bio::SeqIO> and L<Bio::Seq> for more information
=cut
sub read_all_sequences{
my ($filename,$format) = @_;
if( !defined $filename ) {
confess "read_all_sequences($filename) - usage incorrect";
}
my $seqio;
if( defined $format ) {
$seqio = Bio::SeqIO->new( '-file' => $filename, '-format' => $format);
} else {
$seqio = Bio::SeqIO->new( '-file' => $filename);
}
my @seq_array;
while( my $seq = $seqio->next_seq() ) {
push(@seq_array,$seq);
}
return @seq_array;
}
=head2 write_sequence
Title : write_sequence
Usage : write_sequence(">new_file.gb",'genbank',$seq)
write_sequence(">new_file.gb",'genbank',@array_of_sequence_objects)
Function: writes sequences in the specified format
Returns : true
Args : filename as a string, must provide an open() output file
format as a string
one or more sequence objects
=cut
sub write_sequence{
my ($filename,$format,@sequence_objects) = @_;
if( scalar(@sequence_objects) == 0 ) {
confess("write_sequence(filename,format,sequence_object)");
}
my $error = 0;
my $seqname = "sequence1";
# catch users who haven't passed us a filename we can open
if( $filename !~ /^\>/ && $filename !~ /^|/ ) {
$filename = ">".$filename;
}
my $seqio = Bio::SeqIO->new('-file' => $filename, '-format' => $format);
foreach my $seq ( @sequence_objects ) {
my $seq_obj;
if( !ref $seq ) {
if( length $seq > 50 ) {
# odds are this is a sequence as a string, and someone has not figured out
# how to make objects. Warn him/her and then make a sequence object
# from this
if( $error == 0 ) {
carp("WARNING: You have put in a long string into write_sequence.\n".
"I suspect this means that this is the actual sequence\n".
"In the future try the\n".
" new_sequence method of this module to make a new sequence object.\n".
"Doing this for you here\n");
$error = 1;
}
$seq_obj = new_sequence($seq,$seqname);
$seqname++;
} else {
confess("You have a non object [$seq] passed to write_sequence. It maybe that you".
"want to use new_sequence to make this string into a sequence object?");
}
} else {
if( !$seq->isa("Bio::SeqI") ) {
confess("object [$seq] is not a Bio::Seq object; can't write it out");
}
$seq_obj = $seq;
}
# finally... we get to write out the sequence!
$seqio->write_seq($seq_obj);
}
1;
}
=head2 new_sequence
Title : new_sequence
Usage : $seq_obj = new_sequence("GATTACA", "kino-enzyme");
Function: Construct a sequency object from sequence string
Returns : A Bio::Seq object
Args : sequence string
name string (optional, default "no-name-for-sequence")
accession - accession number (optional, no default)
=cut
sub new_sequence{
my ($seq,$name,$accession) = @_;
if( !defined $seq ) {
confess("new_sequence(sequence_as_string) usage");
}
$name ||= "no-name-for-sequence";
my $seq_object = Bio::Seq->new( -seq => $seq, -id => $name);
$accession && $seq_object->accession_number($accession);
return $seq_object;
}
=head2 blast_sequence
Title : blast_sequence
Usage : $blast_result = blast_sequence($seq)
$blast_result = blast_sequence('MFVEGGTFASEDDDSASAEDE');
Function: If the computer has Internet accessibility, blasts
the sequence using the NCBI BLAST server against nrdb.
It chooses the flavour of BLAST on the basis of the sequence.
This function uses Bio::Tools::Run::RemoteBlast, which itself
use Bio::SearchIO - as soon as you want to know more, check out
these modules
Returns : Bio::Search::Result::GenericResult.pm
Args : Either a string of protein letters or nucleotides, or a
Bio::Seq object
=cut
sub blast_sequence {
my ($seq,$verbose) = @_;
if( !defined $verbose ) {
$verbose = 1;
}
if( !ref $seq ) {
$seq = Bio::Seq->new( -seq => $seq, -id => 'blast-sequence-temp-id');
} elsif ( !$seq->isa('Bio::PrimarySeqI') ) {
croak("[$seq] is an object, but not a Bio::Seq object, cannot be blasted");
}
require Bio::Tools::Run::RemoteBlast;
my $prog = ( $seq->alphabet eq 'protein' ) ? 'blastp' : 'blastn';
my $e_val= '1e-10';
my @params = ( '-prog' => $prog,
'-expect' => $e_val,
'-readmethod' => 'SearchIO' );
my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
my $r = $factory->submit_blast($seq);
if( $verbose ) {
print STDERR "Submitted Blast for [".$seq->id."] ";
}
sleep 5;
my $result;
LOOP :
while( my @rids = $factory->each_rid) {
foreach my $rid ( @rids ) {
my $rc = $factory->retrieve_blast($rid);
if( !ref($rc) ) {
if( $rc < 0 ) {
$factory->remove_rid($rid);
}
if( $verbose ) {
print STDERR ".";
}
sleep 10;
} else {
$result = $rc->next_result();
$factory->remove_rid($rid);
last LOOP;
}
}
}
if( $verbose ) {
print STDERR "\n";
}
return $result;
}
=head2 write_blast
Title : write_blast
Usage : write_blast($filename,$blast_report);
Function: Writes a BLAST result object (or more formally
a SearchIO result object) out to a filename
in BLAST-like format
Returns : none
Args : filename as a string
Bio::SearchIO::Results object
=cut
sub write_blast {
my ($filename,$blast) = @_;
if( $filename !~ /^\>/ && $filename !~ /^|/ ) {
$filename = ">".$filename;
}
my $output = Bio::SearchIO->new( -output_format => 'blast', -file => $filename);
$output->write_result($blast);
}
=head2 get_sequence
Title : get_sequence
Usage : $seq_object = get_sequence('swiss',"ROA1_HUMAN");
Function: If the computer has Internet access this method gets
the sequence from Internet accessible databases. Currently
this supports Swissprot ('swiss'), EMBL ('embl'), GenBank
('genbank'), GenPept ('genpept'), and RefSeq ('refseq').
Swissprot and EMBL are more robust than GenBank fetching.
If the user is trying to retrieve a RefSeq entry from
GenBank/EMBL, the query is silently redirected.
Returns : A Bio::Seq object
Args : database type - one of swiss, embl, genbank, genpept, or
refseq
=cut
my $genbank_db = undef;
my $genpept_db = undef;
my $embl_db = undef;
my $swiss_db = undef;
my $refseq_db = undef;
sub get_sequence{
my ($db_type,$identifier) = @_;
if( ! $DBOKAY ) {
confess ("Your system does not have one of LWP, HTTP::Request::Common, IO::String\n".
"installed so the DB retrieval method is not available.\n".
"Full error message is:\n $!\n");
return;
}
$db_type = lc($db_type);
my $db;
if( $db_type =~ /genbank/ ) {
if( !defined $genbank_db ) {
$genbank_db = Bio::DB::GenBank->new();
}
$db = $genbank_db;
}
if( $db_type =~ /genpept/ ) {
if( !defined $genpept_db ) {
$genpept_db = Bio::DB::GenPept->new();
}
$db = $genpept_db;
}
if( $db_type =~ /swiss/ ) {
if( !defined $swiss_db ) {
$swiss_db = Bio::DB::SwissProt->new();
}
$db = $swiss_db;
}
if( $db_type =~ /embl/ ) {
if( !defined $embl_db ) {
$embl_db = Bio::DB::EMBL->new();
}
$db = $embl_db;
}
if( $db_type =~ /refseq/ or ($db_type !~ /swiss/ and
$identifier =~ /^\s*N\S+_/)) {
if( !defined $refseq_db ) {
$refseq_db = Bio::DB::RefSeq->new();
}
$db = $refseq_db;
}
my $seq;
if( $identifier =~ /^\w+\d+$/ ) {
$seq = $db->get_Seq_by_acc($identifier);
} else {
$seq = $db->get_Seq_by_id($identifier);
}
return $seq;
}
=head2 translate
Title : translate
Usage : $seqobj = translate($seq_or_string_scalar)
Function: translates a DNA sequence object OR just a plain
string of DNA to amino acids
Returns : A Bio::Seq object
Args : Either a sequence object or a string of
just DNA sequence characters
=cut
sub translate {
my ($scalar) = shift;
my $obj;
if( ref $scalar ) {
if( !$scalar->isa("Bio::PrimarySeqI") ) {
confess("Expecting a sequence object not a $scalar");
} else {
$obj= $scalar;
}
} else {
# check this looks vaguely like DNA
my $n = ( $scalar =~ tr/ATGCNatgcn/ATGCNatgcn/ );
if( $n < length($scalar) * 0.85 ) {
confess("Sequence [$scalar] is less than 85% ATGCN, which doesn't look very DNA to me");
}
$obj = Bio::PrimarySeq->new(-id => 'internalbioperlseq',-seq => $scalar);
}
return $obj->translate();
}
=head2 translate_as_string
Title : translate_as_string
Usage : $seqstring = translate_as_string($seq_or_string_scalar)
Function: translates a DNA sequence object OR just a plain
string of DNA to amino acids
Returns : A string of just amino acids
Args : Either a sequence object or a string of
just DNA sequence characters
=cut
sub translate_as_string {
my ($scalar) = shift;
my $obj = Bio::Perl::translate($scalar);
return $obj->seq;
}
=head2 reverse_complement
Title : reverse_complement
Usage : $seqobj = reverse_complement($seq_or_string_scalar)
Function: reverse complements a string or sequence argument
producing a Bio::Seq - if you want a string, you
can use reverse_complement_as_string
Returns : A Bio::Seq object
Args : Either a sequence object or a string of
just DNA sequence characters
=cut
sub reverse_complement {
my ($scalar) = shift;
my $obj;
if( ref $scalar ) {
if( !$scalar->isa("Bio::PrimarySeqI") ) {
confess("Expecting a sequence object not a $scalar");
} else {
$obj= $scalar;
}
} else {
# check this looks vaguely like DNA
my $n = ( $scalar =~ tr/ATGCNatgcn/ATGCNatgcn/ );
if( $n < length($scalar) * 0.85 ) {
confess("Sequence [$scalar] is less than 85% ATGCN, which doesn't look very DNA to me");
}
$obj = Bio::PrimarySeq->new(-id => 'internalbioperlseq',-seq => $scalar);
}
return $obj->revcom();
}
=head2 revcom
Title : revcom
Usage : $seqobj = revcom($seq_or_string_scalar)
Function: reverse complements a string or sequence argument
producing a Bio::Seq - if you want a string, you
can use reverse_complement_as_string
This is an alias for reverse_complement
Returns : A Bio::Seq object
Args : Either a sequence object or a string of
just DNA sequence characters
=cut
sub revcom {
return &Bio::Perl::reverse_complement(@_);
}
=head2 reverse_complement_as_string
Title : reverse_complement_as_string
Usage : $string = reverse_complement_as_string($seq_or_string_scalar)
Function: reverse complements a string or sequence argument
producing a string
Returns : A string of DNA letters
Args : Either a sequence object or a string of
just DNA sequence characters
=cut
sub reverse_complement_as_string {
my ($scalar) = shift;
my $obj = &Bio::Perl::reverse_complement($scalar);
return $obj->seq;
}
=head2 revcom_as_string
Title : revcom_as_string
Usage : $string = revcom_as_string($seq_or_string_scalar)
Function: reverse complements a string or sequence argument
producing a string
Returns : A string of DNA letters
Args : Either a sequence object or a string of
just DNA sequence characters
=cut
sub revcom_as_string {
my ($scalar) = shift;
my $obj = &Bio::Perl::reverse_complement($scalar);
return $obj->seq;
}
1;