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Commit 76a7c1ef authored by Sebastien's avatar Sebastien

Use cd-hit to select group representative sequence

parent fc4fc661
......@@ -7,7 +7,7 @@ RUN apt-get -q update && \
hardinfo wget patch vim gawk unzip apache2 zlib1g-dev libpng-dev libgd2-noxpm-dev build-essential && \
apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
RUN apt-get -q update && apt-get install -yq cron at libtree-simple-perl libbio-perl-perl ncbi-blast+ sqlite liberror-perl libswitch-perl libxml-simple-perl libjson-perl libapache-session-perl libnet-ldap-perl libapache-htpasswd-perl ssmtp fasttree mafft biosquid python2.7 python-scipy python-sklearn python-numpy python-fastcluster mcl libarray-utils-perl liburi-encode-perl
RUN apt-get -q update && apt-get install -yq cron at libtree-simple-perl libbio-perl-perl ncbi-blast+ sqlite liberror-perl libswitch-perl libxml-simple-perl libjson-perl libapache-session-perl libnet-ldap-perl libapache-htpasswd-perl ssmtp fasttree mafft biosquid python2.7 python-scipy python-sklearn python-numpy python-fastcluster mcl libarray-utils-perl liburi-encode-perl cd-hit
WORKDIR /var/www/
......
......@@ -66,6 +66,7 @@ sub CreatePanProteome
}
}
}
$h_list_group_select_seqid_code{$groupid} = &SelectSequenceRepGroupe($rh_species, \@a_allseqs1);
}
......@@ -80,7 +81,7 @@ sub CreatePanProteome
Title : SelectSequenceRepGroupe
Usage : @selec = &SelectSequenceRepGroupe($rh_species,\@a_allseqs1);
Prerequisite : none
Function : Select representative sequence
Function : Select representative sequence [longest from cdhit 50 cluster]
Returns : array of [code,seqid]
Args : hash of species, array of array of [code,seqid]
Globals : none
......@@ -89,35 +90,40 @@ sub CreatePanProteome
sub SelectSequenceRepGroupe
{
my ($rh_species, $SeqForSelect) = @_;
my ($rh_species, $ra_species_seqid_list) = @_;
my $selecSeqid = "";
my $selecCode = "";
foreach my $toselect (@{$SeqForSelect})
my ($fh_tmp, $tmpfile) = File::Temp::tempfile(UNLINK => 1);
foreach my $ra_species_seqid (@{$ra_species_seqid_list})
{
if ($selecSeqid eq "")
{
$selecSeqid = $toselect->[1];
$selecCode = $toselect->[0];
}
else
{
my $nb_X_selec = ($rh_species->{$selecCode}->{'sequences'}->{$selecSeqid}->{'sequence'} =~ tr/X/X/);
my $nb_X_toselec =
($rh_species->{$toselect->[0]}->{'sequences'}->{$toselect->[1]}->{'sequence'} =~ tr/X/X/);
if (
(
length($rh_species->{$toselect->[0]}->{'sequences'}->{$toselect->[1]}->{'sequence'}) -
$nb_X_toselec * 3
) > (length($rh_species->{$selecCode}->{'sequences'}->{$selecSeqid}->{'sequence'}) - $nb_X_selec * 3)
)
{
$selecSeqid = $toselect->[1];
$selecCode = $toselect->[0];
}
}
}
return [$selecSeqid, $selecCode];
my $species_code = $ra_species_seqid->[0];
my $seqid = $ra_species_seqid->[1];
my $sequence = $rh_species->{$species_code}->{'sequences'}->{$seqid}->{'sequence'};
print $fh_tmp <<END;
>$species_code|$seqid acc=$seqid sp=$species_code
$sequence
END
}
$fh_tmp->close();
my $cdhit_cmd = "cdhit -i $tmpfile -o $tmpfile.cdhit -c 0.5 -n 3";
&System("($cdhit_cmd > /dev/null ) 2> /dev/null");
my %h_cdhit = ();
&FastaToHash("$tmpfile.cdhit",\%h_cdhit, 'noseq');
my $longest = 0;
my $representative;
foreach my $cdhit_seq (keys %h_cdhit)
{
my $len = $h_cdhit{$cdhit_seq}->{len};
if ($len > $longest)
{
$longest = $len;
$representative = $cdhit_seq;
}
}
return [$h_cdhit{$representative}->{'acc'}, $h_cdhit{$representative}->{'sp'}];
}
=head3 function PrintPanProteome
......
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