Commit 58fc5cb7 authored by Sebastien's avatar Sebastien

Core proteome

parent 75c15575
This diff is collapsed.
......@@ -118,6 +118,23 @@ sub PrintOrthologousProteinsFiles
&__PrintSpecificProteinsFilesByType("$outdir/orthologous_proteins",$rh_species,$rh_orthologous,'orthologous');
my %h_coreproteome = ();
foreach my $code (keys %{$rh_species})
{
$h_coreproteome{$code} = '';
foreach my $seqid (sort { $rh_orthologous->{$code}->{$a}->{'groupid'} cmp $rh_orthologous->{$code}->{$b}->{'groupid'} } keys %{$rh_orthologous->{$code}})
{
$h_coreproteome{$code} .= $rh_orthologous->{$code}->{$seqid}->{'sequence'};
}
}
my $fh_coreproteome = &GetStreamOut("$outdir/orthologous_proteins/core.proteome.fasta");
foreach my $code (keys %h_coreproteome)
{
my $seq = $h_coreproteome{$code};
$seq = &FormatSeq(\$seq);
print $fh_coreproteome ">$code\n$seq\n";
}
$fh_coreproteome->close;
return;
}
......
......@@ -108,15 +108,6 @@ IADASVVIQSAIRGWLVRRCSGDIGWLKSGGAKTNELGEVLVKASVLSELQRRVLKAEAALREKEEENDI
LQQRLQQYENRWSEYETKMKSMEEIWQKQMRSLQSSLSIAKKSLAVEDSARNSDASVNASDATDWDSSSN
QFRSQTSNGVGSRLQPMSAGLSVIGRLAEEFEQRAQVFGDDAKFLVEVKSGQVEANLDPDRELRRLKQMF
ETWKKDYGGRLRETKLILSKLGSEESSGSMEKVKRKWWGRRNSTRY
>At3g45690
MARSVDTEAMTTRDPSSKRGGWKTFPFMIATLLGLSIASFGWVMNLVVFLIKEFNIKSIAATQNSNIVNG
CVSMLPVVAAILADSFFGNIPVISVSAFISLLGIILLTMITSLDHLRPPPCETGSILCESPSKLQLGILY
IALALVIIGSAGTRFTLASAGANQYEKPKEQGSFFNWYFLTLYTGAITGATAIVYTQENASWKLGFGLCA
VANLISFIVFVSGKRYYKHDKPMGSPFTNLIRVVVAATRKRKAVISSREEDYHHGLGREGKTSSAMPSKS
FRFFNRAALKTEDDSVNNNWRLCSVQEVEDFKAVFRVLPLLLAIIFVSTPMVTQTSLIILQALVTDRGLG
PHFKIPAGSLQVIVIITACIVILMNNCLVYPMYQKLAHKPLTPLQKVGIGHVFIILSMAISAIVEAKRLK
TVTNGHSMSVLWLHRDFIASVVIGISFYLSTALITLIQKTTKWLPNDINHGRVDNVYWLLVIVGVLNYFL
VCAWFYRYRNLNDDDDQEQDPKDDTT
>At5g20490
MKETEGNAQCYAIFVVFLINIIVGSHVWIEDPGAAWIDGEVVKINGEEVHAHTTNGKTVVANIANVFPKD
TEAPPGGVDDMTKLSYLHEPGVLNNLAMRYELNEIYTYTGNILIAVNPFQRLPHLYDTHMMEQYKGAGFG
......@@ -175,3 +166,5 @@ QSAVRGWLARKHFNSMQRQKELRNVATKSKRKAGRRISEDKDIPLEQPQVQPTSMSDLQKRILKSEAALS
QKEEENTALREQLRQFEERWSEYDIKMKSMEETWQKQMSSLQMSLAAARKSLAAESITGQAGGRQDTSIS
PFGYDSEDTMSTGTPGVRTPTNKFTNGNTPELRIRELNGSLNAVNHLAREFDQRRLNFDEDARAIVEVKL
GPQATPNGQQQQHPEDEFRRLKLRFETWKKDYKARLRDTKARLHRVDGDKGRHRKWWGKRG
>specificAA
ARRRRRRAAARAERRRXXXARARRXRRXAXXRRRAXARRXAXXXXAAX
......@@ -2,7 +2,7 @@
"contact" : "sebastien.carrere@toulouse.inra.fr",
"title" : "Low Stringency analysis test",
"orthomcl" : {
"parameters" : " --pmatch_cutoff=60 "
"parameters" : " --pmatch_cutoff=80"
},
"proteomes" : {
"yeast" : {
......
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