BioPerl and other useful Perl approaches for bioinformaticians

Toni Hermoso Pulido

@toniher

Perlbrew

Install different Perl versions as a normal user

http://perlbrew.pl/

Install Perlbrew

\curl -L http://install.perlbrew.pl | bash

Install and use Perl versions

# Install a Perl version
perlbrew install perl-5.22.0

# Switch definitely to that version
perlbrew switch perl-5.22.0

# Use only during that session
perlbrew use perl-5.22.0

Install Perl modules

cpanm (cpannmins)

 

#Install CSV
cpanm CSV

#Install BioPerl
cpanm BioPerl

If things do not work, you always have classical cpan (interactive commandline)

Update Perl modules

# Install cpanoutdated package
cpanm App::cpanoutdated

# Update list of outdated modules
cpan-outdated -p | cpanm

Reinstall modules between versions

# Use a specific Perl version
perlbrew use perl-5.8.8
# List installed modules
perlbrew list-modules


# Install modules of current Perl version into another specific one
perlbrew list-modules | perlbrew exec --with perl-5.16.2 cpanm

http://perlbrew.pl/Reinstall-All-Modules-On-New-Perl.html

Perl one-liners

awk/sed on steroids

Example file:

ftp://ftp.ensembl.org/pub/release-82/gtf/felis_catus/Felis_catus.Felis_catus_6.2.82.gtf.gz

GTF (tab-separated-like format with gene structure information)

perl -e

perl -e 'print "Hello world!";'

-e: execute

perl -p

perl -p -e '$_=~s/exon/intron/;' \
Felis_catus.Felis_catus_6.2.82.gtf

-p: print

perl -n

perl -p -n -e '$_= $_."\tMore"' \
Felis_catus.Felis_catus_6.2.82.gtf

# Alternative
perl -n -e 'print $_."\tMore"' \
Felis_catus.Felis_catus_6.2.82.gtf

-n: handle newline characters

perl -l

perl -p -l -n -e '$_= $_."\tMore"' \
Felis_catus.Felis_catus_6.2.82.gtf

# Alternative
perl -n -l -e 'print $_."\tMore"' \
Felis_catus.Felis_catus_6.2.82.gtf

-l: chomp newline characters

perl -a

-a: autosplit (default whitespaces). Put into @F array

perl -lane 'print $F[2].":".$F[6]' \
Felis_catus.Felis_catus_6.2.82.gtf

perl -F

perl -F\; -lane  'print $F[1]' \
Felis_catus.Felis_catus_6.2.82.gtf

# Some extra processing
perl -F\; -lane  '($num) = $F[1] =~/(\d+)/; \
print "Version: ".$num; ' \
Felis_catus.Felis_catus_6.2.82.gtf

-F: with autosplit (choice of separator)

perl -s

perl -s -F\; -lane  '($num) = $F[1] =~/(\d+)/; \
print "$desc: $extra ".$num; ' -- -desc=Tal \
-extra=Number Felis_catus.Felis_catus_6.2.82.gtf

-s: Pass parameters

perl -i

perl -i.backup -p -lane  's/exon/intron/g;' \
Felis_catus.Felis_catus_6.2.82.gtf

-in: Operate in-place

References

 

 

Code snippets at:

https://github.com/toniher/perl-bioinformatics

Useful Perl Modules

You don't need to reinvent the wheel

Data::Dumper

#!/usr/bin/env perl

use Data::Dumper;

# Data structure
my %gene = ( 
    "gene" => "BRCA",
    "position" => {
            "start" => 4400, 
            "end" => 8005 
    }
);


# NO
print Dumper(%gene);

# YES
print Dumper(\%gene);

Text::Trim

#!/usr/bin/env perl

use Text::Trim qw( trim ltrim rtrim );

my $text = " That's all folks! ";

print "*".ltrim( $text )."*\n";
print "*".rtrim( $text )."*\n";
print "*".trim( $text )."*\n";

print "*".$text."*\n";

trim( $text );

print "*".$text."*\n";

http://perlmaven.com/trim

Text::CSV (Text::CSV_XS)

#!/usr/bin/env perl

use strict;
use warnings;
use 5.010; #Version 5.10 at least
use Text::CSV;

my $file = $ARGV[0] // "file.csv";
my $csv = Text::CSV->new ( { binary => 1, sep_char => "\t", 
            quote_char => "", empty_is_undef => 1 } )
            or die "Cannot use CSV: ".Text::CSV->error_diag ();

open my $fh, "<:encoding(utf8)", "$file" or die "$file: $!";

while ( my $row = $csv->getline( $fh ) ) {

	if ( $row->[2] ) {
		print $row->[2].": ".$row->[3]."-".$row->[4]."\n";
		my $list = [ $row->[2], $row->[3], $row->[4] ];
		push( @rows, $list );
	}
}

close $fh;

Text::CSV (Text::CSV_XS)

my $csvout = Text::CSV->new ( { binary => 1, sep_char => ",", 
                quote_char => '\"', eol => "\n" } )
                or die "Cannot use CSV: ".Text::CSV->error_diag ();

open my $fhout, ">:encoding(utf8)", "out.csv" or die "out.csv: $!";

while ( my $row = shift( @rows ) ) {
	$csvout->print($fhout, $row );
}



close $fhout;

More info on parameters...

Other modules

 

  • DBI (e.g. DBD::SQLite)
  • GetOpt
  • Config::JSON
  • etc.

Access to (biological) webservices

Example

ENSEMBL REST API

http://rest.ensembl.org/documentation/info/taxonomy_id

HTTP::Tiny

#!/usr/bin/env perl

use strict;
use warnings;

use Data::Dumper;
 
use HTTP::Tiny;
 
my $http = HTTP::Tiny->new();
 
my $server = 'http://rest.ensembl.org';
my $ext = '/taxonomy/id/9606?';
my $response = $http->get($server.$ext, {
  headers => { 'Content-type' => 'application/json' }
});
 
die "Failed!\n" unless $response->{success};


print Dumper( $response );

HTTP::Tiny vs LWP:UserAgent

JSON (JSON::XS)

use JSON;

if(length $response->{content}) {
  my $hash = decode_json($response->{content});

  print $hash->{"scientific_name"}, "\n";

}

BioPerl

http://www.bioperl.org

Bio::Seq

#!/usr/bin/env perl

use Bio::Seq;
use Data::Dumper;

# http://search.cpan.org/dist/BioPerl/Bio/Seq.pm
my $seqobj = Bio::Seq->new( -display_id => 'MySEQ001',
	-seq => "GATACAGATACA",
	-desc => "New sequence"
);

print Dumper( $seqobj );

Bio::Seq::Feature::Generic

use Bio::SeqFeature::Generic;

# http://search.cpan.org/dist/BioPerl/Bio/SeqFeature/Generic.pm
my $feat = Bio::SeqFeature::Generic->new( 
    -start        => 10, 
    -end          => 100,
    -strand       => -1, 
    -primary      => 'repeat', # -primary_tag is a synonym
    -source_tag   => 'repeatmasker',
    -display_name => 'alu family',
    -score        => 1000,
    -tag          => { new => 1,
                       author => 'someone',
                       sillytag => 'this is silly!' } );

$seqobj->add_SeqFeature($feat);

print Dumper( $seqobj );

FASTA

>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
IENY
>gi|2055231|dbj|AB000263.1| Homo sapiens mRNA for prepro cortistatin like peptide, complete cds
ACAAGATGCCATTGTCCCCCGGCCTCCTGCTGCTGCTGCTCTCCGGGGCCACGGCCACCGCTGCCCTGCC
CCTGGAGGGTGGCCCCACCGGCCGAGACAGCGAGCATATGCAGGAAGCGGCAGGAATAAGGAAAAGCAGC
CTCCTGACTTTCCTCGCTTGGTGGTTTGAGTGGACCTCCCAGGCCAGTGCCGGGCCCCTCATAGGAGAGG
AAGCTCGGGAGGTGGCCAGGCGGCAGGAAGGCGCACCCCCCCAGCAATCCGCGCGCCGGGACAGAATGCC
CTGCAGGAACTTCTTCTGGAAGACCTTCTCCTCCTGCAAATAAAACCTCACCCATGAATGCTCACGCAAG
TTTAATTACAGACCTGAA

Amino acid sequence

Nucleotide sequence

Bio::SeqIO

#!/usr/bin/env perl

use Bio::SeqIO;

$in  = Bio::SeqIO->new(-file => "nucl.fasta" ,
                       -format => 'Fasta');


while ( my $seq = $in->next_seq() ) {
	print "* ", $seq->display_name(), " - ";
        print $seq->desc(), "\n";
	print $seq->seq(), "\n";
}

Bio::SeqIO

use Bio::SeqIO;

my $outfasta  = Bio::SeqIO->new(-file => ">myseq.fasta" ,
                       -format => 'Fasta');


$outfasta->write_seq($seqobj);

my $outembl  = Bio::SeqIO->new(-file => ">myseq.embl" ,
                       -format => 'EMBL');
                       
$outembl->write_seq($seqobj);

FASTQ

@M03766:3:000000000-ADALA:1:1101:19359:1544 1:N:0:98
ACTACGGGAGGCTGCAGTAGGGAATCTTCGGCAATGGGGGCAACCCTGACCGAGCAACGCCGCGTGAGTGATGAAGGTTTTCGGATCGTAAAGCTCTTTTGTTATTTAAGAACGAGTGTCTGCGTGCACCTTTCTCACTTTCCCGGTACCTTACCAGAAACCCCCGCCTATCTACTTCCCACCAGCCGCGCTATTCCGTAGGTCCCGATCGTTGTCCGGTTTTCTTTGCCTTCAAGCGAGCCCTGCCGGTTCTTTAATTCTGTTTTTAATGCCTGTGCCTTCCCCTTTCTCCTCTTTTTTT
+
-8ACCE385>5=;===CE9EGGFFGGGGF@,FGCFGGA,@BFGD6FGGE6C68FFFF@F@FGGGGE,,CEA,<,,5C,,9AF:>+B78B,,:,9BE?,C<,:,9,,,,,,,,:+++8+:,,,,+8+++,,,3,:,3,:>,:,,:++3++5338>3,,,,,,,**5**/1*,7,,5,3,?<<,=,,,41*1*1**++322((*5:2/*0)-*2/*260**)1/1*3<+++-*2*+2*))(*()((/*.((2.(*)0**)2-1*)+*20.+)),.0*+++))++,20,0+)***+.030+,**
!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNO
PQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~

Quality

Bio::SeqIO - FASTQ

#!/usr/bin/env perl

use Bio::SeqIO;
use Data::Dumper;

# http://search.cpan.org/dist/BioPerl/Bio/SeqIO/fastq.pm
$in  = Bio::SeqIO->new(-file => "example.fastq" ,
                       -format => 'Fastq');


while ( my $seq = $in->next_seq() ) {
	# Bio::Seq::Quality object
	# http://search.cpan.org/dist/BioPerl/Bio/Seq/Quality.pm
	print "* ", $seq->display_name(), "\n";
	print $seq->seq(), "\n";
	print $seq->qual_text(), "\n";
	print join( ",", @{$seq->qual()} ), "\n";
}

Other modules

  • Bio::Align and Bio::AlignIO (seq alignments)
  • Bio::FeatureIO (read/write GTF, GFF, etc.)
  • Bio::Ontology (Ontology terms, e. g. GO)
  • Bio::Tree and Bio::TreeIO (phylogenetic trees)
  • Bio::Tools (specific parsers or wrappers of applications)

NCBI Entrez

PubMed

Bio::Biblio

cpanm Bio::Biblio

PubMed eutils retrieval

#!/usr/bin/env perl

use Bio::Biblio;
use Bio::Biblio::IO;
use Bio::Biblio::Ref;


my $biblio = Bio::Biblio->new( -access => 'eutils' );
$biblio->find("Hermoso A [au] OR Hermoso T [au]");
while ( my $xml = $biblio->get_next ) {
	# Handling in Biblio IO 
	my $io = Bio::Biblio::IO->new( -data => $xml,
                             -format => 'medlinexml' );

	# Handling Biblio Ref
	while ( my $article = $io->next_bibref() ) {
		print "* ", $article->title, "\n";
		print $article->abstract, "\n\n";
	}

}

Get sequences from Genbank

#!/usr/bin/env perl

use Bio::DB::GenBank;

my $gb = Bio::DB::GenBank->new();

# http://search.cpan.org/dist/BioPerl/Bio/Seq/RichSeq.pm
my $seq = $gb->get_Seq_by_gi('5524211'); # GI Number

# my $seq = $gb->get_Seq_by_acc('AAD44166'); # Acc Number
# my $seq = $gb->get_Seq_by_version('AAD44166.1'); # Acc.version

# Get sequence and sequence information
print $seq->molecule(), "\n";
print $seq->display_name(), "\n";
print $seq->seq(), "\n";
print $seq->description(), "\n";

# Fasta file
my $out = Bio::SeqIO->new(-file => ">out.fasta" ,
                          -format => 'fasta');
$out->write_seq($seq->primary_seq);

ENSEMBL Perl API

http://www.ensembl.org/info/docs/api/index.html

Installation Core API

# Assuming BioPerl is installed and installing in $HOME

cd $HOME

git clone https://github.com/Ensembl/ensembl-git-tools.git


export PATH=$PWD/ensembl-git-tools/bin:$PATH

git ensembl --clone api

# Load ENSEMBL Modules
export PERL5LIB=${PERL5LIB}:${HOME}/ensembl/modules

Overview

http://www.ensembl.org/info/docs/api/core/core_API_diagram.html

List adaptors

use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
    -host => 'ensembldb.ensembl.org',
    -user => 'anonymous'
);

my @db_adaptors = @{ $registry->get_all_DBAdaptors() };

foreach my $db_adaptor (@db_adaptors) {
    my $db_connection = $db_adaptor->dbc();

    printf(
        "species/group\t%s/%s\ndatabase\t%s\nhost:port\t%s:%s\n\n",
        $db_adaptor->species(),   $db_adaptor->group(),
        $db_connection->dbname(), $db_connection->host(),
        $db_connection->port()
    );
}

Retrieval of genes and others

my $slice_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Slice' );
my $slice = $slice_adaptor->fetch_by_region( 'chromosome', 'X', 1e6, 10e6 );

my $genes = $slice->get_all_Genes();
while ( my $gene = shift @{$genes} ) {
    my $gstring = feature2string($gene);
    print "$gstring\n";

    my $transcripts = $gene->get_all_Transcripts();
    while ( my $transcript = shift @{$transcripts} ) {
        my $tstring = feature2string($transcript);
        print "\t$tstring\n";

        foreach my $exon ( @{ $transcript->get_all_Exons() } ) {
            my $estring = feature2string($exon);
            print "\t\t$estring\n";
        }
    }
}

Feature data

sub feature2string
{
    my $feature = shift;

    my $stable_id  = $feature->stable_id();
    my $seq_region = $feature->slice->seq_region_name();
    my $start      = $feature->start();
    my $end        = $feature->end();
    my $strand     = $feature->strand();

    return sprintf( "%s: %s:%d-%d (%+d)",
        $stable_id, $seq_region, $start, $end, $strand );
}

ENSEMBL API Tutorial

 

http://www.ensembl.org/info/docs/api/core/core_tutorial.html

Questions?

BioPerl and other useful Perl approaches for bioinformaticians‎

By Similis.cc

BioPerl and other useful Perl approaches for bioinformaticians‎

In this hands-on workshop (laptop recommended) we will introduce the following topics: perlbrew, Perl one-liners: awk/sed on steroids, some useful Perl modules for Bioinformatics, I/O of Bioinformatics formats, Access to Bioinformatics web services (NCBI Entrez, ENSEMBL)

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