/
gb2db.pl
executable file
·1077 lines (958 loc) · 42.5 KB
/
gb2db.pl
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#!/usr/bin/env perl
use Bio::SeqIO;
use Bio::Perl;
use Bio::DB::GenBank;
use Pod::Usage;
use Getopt::Long;
use File::Temp qw/ tempfile tempdir /;
use Storable qw(freeze thaw);
use Data::Dumper;
use IO::Compress::RawDeflate qw(rawdeflate $RawDeflateError);
use IO::Uncompress::RawInflate qw(rawinflate $RawInflateError);
use strict;
my $in_file = "";
my $out_file = "";
my $snp_list = "";
my $version = "0.2.170415";
my $line = "-" x 50;
my $strain_name = "";
my $organism_name = "";
my $organism_id = "";
my $remote = 0;
GetOptions(
'i=s' => \$in_file,
'o=s' => \$out_file,
'id=s' => \$organism_id,
'snp=s' => \$snp_list
# 'c=s' => \$codon_file,
);
if ( $in_file ne "" and $out_file ne "" ) {
&create_db_file;
}
elsif ( $in_file eq "" and $out_file ne "" and $organism_id ne "" ) {
#
my $gb_file = "$organism_id.gb";
if ( -e $gb_file ) {
print
"The file $gb_file already exists. If you want to use it press Y. If you want to download it again press N. Press X to exit.\n";
my $input = uc(<STDIN>);
chomp $input;
if ( $input eq "N" || $input eq "NO" ) {
$remote = 1;
&create_db_file;
}
elsif ( $input eq "Y" || $input eq "YES" ) {
$remote = 0;
$in_file = $gb_file;
&create_db_file;
}
}
else {
$remote = 1;
&create_db_file;
}
}
else {
print
"$line\nUsage: gb2db.pl -i GENBANK_FILE -o OUT_FILE\n$line\nver.$version\n";
}
sub create_db_file {
my (%annotations, $gene_feature, $start, $end,
$tag, $locus_tag, $gene, $gene_synonym,
$protein_id, $product, $note, $translation_table,
$seqobj, $feat, $tag_value, $nucleotide,
$count_genes, $loc_strand, %dict, $seqio_object
);
if ( $remote == 0 ) {
print "Parsing of $in_file file...\n";
$seqio_object = Bio::SeqIO->new( -file => $in_file );
}
elsif ( $remote == 1 ) {
print "Downloading $organism_id file from GenBank server...\n";
my $genBank
= new Bio::DB::GenBank; # This object knows how to talk to GenBank
my $seq = $genBank->get_Seq_by_acc($organism_id)
; # get a record by accession
my $out_file = "$organism_id.gb";
my $seq_object = Bio::SeqIO->new(
-format => 'genbank',
'-file' => ">$out_file",
-verbose => -1
);
$seq_object->write_seq($seq);
print "The file saved as $out_file\n";
$seqio_object = Bio::SeqIO->new( -file => $out_file );
# my $seqio_object = Bio::SeqIO->new(-format => 'genbank');
# while ( my $seq = $in->next_seq() ) {
# $out->write_seq($seq);
# }
# $seqio_object->write_seq($seq);
}
my $seq_object = $seqio_object->next_seq;
# my $genome_seq = $seq_object->seq();
my $genome_seq_obj = Bio::Seq->new( -seq => $seq_object->seq() );
my $display_id = $seq_object->display_id();
my $genome_length = $seq_object->length();
my $nuc_seq = "";
my $rev_seq = "";
print "-" x 50 . "\n";
for my $feat_object ( $seq_object->get_SeqFeatures ) {
if ( $feat_object->strand != 0 ) {
$loc_strand = $feat_object->strand, "\n"; # -1,1
}
if ( $feat_object->primary_tag eq "source" ) {
for my $val ( $feat_object->get_tag_values('organism') ) {
$organism_name = $val;
print "Organism: $organism_name\n";
}
for my $val ( $feat_object->get_tag_values('strain') ) {
$strain_name = $val;
print "Strain: $strain_name\n";
}
}
if ( $feat_object->primary_tag eq "CDS"
|| $feat_object->primary_tag eq "rRNA"
|| $feat_object->primary_tag eq "tRNA" )
{
$start = $feat_object->location->start;
$end = $feat_object->location->end;
$count_genes++;
# print "start: $start\nstop: $end\n";
# my $gene_length = ( $end - $start ) + 1;
# my $gene_seq = substr( $genome_seq, $start - 1,
# $gene_length );
if ( $feat_object->has_tag('gene') ) {
for my $val ( $feat_object->get_tag_values('gene') ) {
# print "gene: ", $val, "\n";
$gene = $val;
# $count_genes++;
# e.g. 'NDP', from a line like '/gene="NDP"'
}
}
if ( $feat_object->has_tag('locus_tag') ) {
for my $val ( $feat_object->get_tag_values('locus_tag') ) {
# print "locus_tag: ", $val, "\n";
$locus_tag = $val;
# e.g. 'NDP', from a line like '/gene="NDP"'
}
}
if ( $feat_object->has_tag('note') ) {
for my $val ( $feat_object->get_tag_values('note') ) {
# print "note: ", $val, "\n";
$note = $val;
# e.g. 'NDP', from a line like '/gene="NDP"'
}
}
if ( $feat_object->has_tag('product') ) {
for my $val ( $feat_object->get_tag_values('product') ) {
# print "product: ", $val, "\n";
$product = $val;
# e.g. 'NDP', from a line like '/gene="NDP"'
}
}
if ( $feat_object->has_tag('transl_table') ) {
for my $val ( $feat_object->get_tag_values('transl_table') ) {
# print "translation:\n", $val, "\n";
$translation_table = $val;
# e.g. 'NDP', from a line like '/gene="NDP"'
}
}
if ( $loc_strand == 1 ) {
$nuc_seq = $genome_seq_obj->subseq( $start, $end );
}
elsif ( $loc_strand == -1 ) {
$nuc_seq
= revcom( $genome_seq_obj->subseq( $start, $end ) )
->seq();
}
# $reverse_complement = revcom( $sequence );
$annotations{$locus_tag}{gene} = $gene;
# $annotations{$locus_tag}{gene_synonym} = $gene_synonym;
$annotations{$locus_tag}{product} = $product;
# $annotations{$locus_tag}{protein_id} = $protein_id;
$annotations{$locus_tag}{start} = $start;
$annotations{$locus_tag}{end} = $end;
$annotations{$locus_tag}{note} = $note;
$annotations{$locus_tag}{transl_table} = $translation_table;
$annotations{$locus_tag}{strand} = $loc_strand;
$annotations{$locus_tag}{sequence} = $nuc_seq;
# $annotations{$locus_tag}{nc} = $gene_seq;
#TANG
#-------------------------------------
# %hash = map { get_a_key_for($_) => $_ } @array;
# %new_hash = map { new_key($_) => new_value($hash{$_}) } keys %hash;
# my @tmp_tang= qw /ST QP EA LH RL VI SG SC KM GC SA AS QH RS RP PL NS VL RT EG RC DE RH IM VF NY IL AP QL EK SW NT KN LW DG SF YF RQ PH IF DV EQ SP TI SI CF LM AV LF GV NI TA DN SL RG CW RK TM KI EV CY KQ TP HY SY RW NH KT DA RI GW GA VM DH RM DY HF EH YQ IQ AR W E G Q Y/;
# my %tmp_tang_h= map {tang($_) => $_} @tmp_tang;
${dict}{tang}{ST} = 2.490;
${dict}{tang}{QP} = 1.377;
${dict}{tang}{EA} = 0.906;
${dict}{tang}{LH} = 0.560;
${dict}{tang}{RL} = 0.414;
${dict}{tang}{VI} = 2.415;
${dict}{tang}{SG} = 1.360;
${dict}{tang}{SC} = 0.852;
${dict}{tang}{KM} = 0.559;
${dict}{tang}{GC} = 0.414;
${dict}{tang}{SA} = 2.380;
${dict}{tang}{AS} = 2.380;
${dict}{tang}{QH} = 1.351;
${dict}{tang}{RS} = 0.850;
${dict}{tang}{RP} = 0.559;
${dict}{tang}{PL} = 0.388;
${dict}{tang}{NS} = 2.053;
${dict}{tang}{VL} = 1.329;
${dict}{tang}{RT} = 0.827;
${dict}{tang}{EG} = 0.553;
${dict}{tang}{RC} = 0.382;
${dict}{tang}{DE} = 2.033;
${dict}{tang}{RH} = 1.317;
${dict}{tang}{IM} = 0.827;
${dict}{tang}{VF} = 0.548;
${dict}{tang}{NY} = 0.378;
${dict}{tang}{IL} = 1.726;
${dict}{tang}{AP} = 1.288;
${dict}{tang}{QL} = 0.805;
${dict}{tang}{EK} = 0.548;
${dict}{tang}{SW} = 0.375;
${dict}{tang}{NT} = 1.695;
${dict}{tang}{KN} = 1.075;
${dict}{tang}{LW} = 0.793;
${dict}{tang}{DG} = 0.548;
${dict}{tang}{SF} = 0.365;
${dict}{tang}{YF} = 1.649;
${dict}{tang}{RQ} = 1.045;
${dict}{tang}{PH} = 0.784;
${dict}{tang}{IF} = 0.545;
${dict}{tang}{DV} = 0.361;
${dict}{tang}{EQ} = 1.634;
${dict}{tang}{SP} = 1.039;
${dict}{tang}{TI} = 0.750;
${dict}{tang}{SI} = 0.540;
${dict}{tang}{CF} = 0.321;
${dict}{tang}{LM} = 1.601;
${dict}{tang}{AV} = 1.017;
${dict}{tang}{LF} = 0.732;
${dict}{tang}{GV} = 0.539;
${dict}{tang}{NI} = 0.321;
${dict}{tang}{TA} = 1.587;
${dict}{tang}{DN} = 1.015;
${dict}{tang}{SL} = 0.725;
${dict}{tang}{RG} = 0.534;
${dict}{tang}{CW} = 0.271;
${dict}{tang}{RK} = 1.583;
${dict}{tang}{TM} = 1.007;
${dict}{tang}{KI} = 0.688;
${dict}{tang}{EV} = 0.506;
${dict}{tang}{CY} = 0.268;
${dict}{tang}{KQ} = 1.466;
${dict}{tang}{TP} = 1.001;
${dict}{tang}{HY} = 0.665;
${dict}{tang}{SY} = 0.503;
${dict}{tang}{RW} = 0.263;
${dict}{tang}{NH} = 1.382;
${dict}{tang}{KT} = 0.989;
${dict}{tang}{DA} = 0.657;
${dict}{tang}{RI} = 0.490;
${dict}{tang}{GW} = 0.242;
${dict}{tang}{GA} = 1.379;
${dict}{tang}{VM} = 0.986;
${dict}{tang}{DH} = 0.560;
${dict}{tang}{RM} = 0.470;
${dict}{tang}{DY} = 0.241;
${dict}{tang}{HF} = '';
${dict}{tang}{EH} = '';
${dict}{tang}{YQ} = '';
${dict}{tang}{IQ} = '';
${dict}{tang}{AR} = '';
${dict}{tang}{W} = '';
${dict}{tang}{E} = '';
${dict}{tang}{G} = '';
${dict}{tang}{Q} = '';
${dict}{tang}{Y} = '';
# Sneath dic
#----------------------------------------
${dict}{sneath}{LI} = '0.889';
${dict}{sneath}{LV} = '0.785';
${dict}{sneath}{LG} = '0.380';
${dict}{sneath}{LA} = '0.643';
${dict}{sneath}{LP} = '0.432';
${dict}{sneath}{LQ} = '0.501';
${dict}{sneath}{LN} = '0.506';
${dict}{sneath}{LM} = '0.515';
${dict}{sneath}{LT} = '0.432';
${dict}{sneath}{LS} = '0.411';
${dict}{sneath}{LC} = '0.398';
${dict}{sneath}{LE} = '0.333';
${dict}{sneath}{LD} = '0.387';
${dict}{sneath}{LK} = '0.492';
${dict}{sneath}{LR} = '0.360';
${dict}{sneath}{LY} = '0.347';
${dict}{sneath}{LF} = '0.570';
${dict}{sneath}{LW} = '0.368';
${dict}{sneath}{LH} = '0.450';
${dict}{sneath}{IV} = '0.843';
${dict}{sneath}{IG} = '0.371';
${dict}{sneath}{IA} = '0.588';
${dict}{sneath}{IP} = '0.419';
${dict}{sneath}{IQ} = '0.453';
${dict}{sneath}{IN} = '0.456';
${dict}{sneath}{IM} = '0.494';
${dict}{sneath}{IT} = '0.493';
${dict}{sneath}{IS} = '0.360';
${dict}{sneath}{IC} = '0.348';
${dict}{sneath}{IE} = '0.366';
${dict}{sneath}{ID} = '0.338';
${dict}{sneath}{IK} = '0.477';
${dict}{sneath}{IR} = '0.342';
${dict}{sneath}{IY} = '0.266';
${dict}{sneath}{IF} = '0.487';
${dict}{sneath}{IW} = '0.287';
${dict}{sneath}{IH} = '0.368';
${dict}{sneath}{VG} = '0.437';
${dict}{sneath}{VA} = '0.675';
${dict}{sneath}{VP} = '0.473';
${dict}{sneath}{VQ} = '0.416';
${dict}{sneath}{VN} = '0.395';
${dict}{sneath}{VM} = '0.465';
${dict}{sneath}{VT} = '0.551';
${dict}{sneath}{VS} = '0.439';
${dict}{sneath}{VC} = '0.430';
${dict}{sneath}{VE} = '0.239';
${dict}{sneath}{VD} = '0.279';
${dict}{sneath}{VK} = '0.419';
${dict}{sneath}{VR} = '0.307';
${dict}{sneath}{VY} = '0.199';
${dict}{sneath}{VF} = '0.380';
${dict}{sneath}{VW} = '0.195';
${dict}{sneath}{VH} = '0.3';
${dict}{sneath}{GA} = '0.659';
${dict}{sneath}{GP} = '0.499';
${dict}{sneath}{GQ} = '0.163';
${dict}{sneath}{GN} = '0.19';
${dict}{sneath}{GM} = '0.149';
${dict}{sneath}{GT} = '0.396';
${dict}{sneath}{GS} = '0.323';
${dict}{sneath}{GC} = '0.29';
${dict}{sneath}{GE} = '0.049';
${dict}{sneath}{GD} = '0.015';
${dict}{sneath}{GK} = '0.309';
${dict}{sneath}{GR} = '0.149';
${dict}{sneath}{GY} = '0.163';
${dict}{sneath}{GF} = '0.259';
${dict}{sneath}{GW} = '0.138';
${dict}{sneath}{GH} = '0.183';
${dict}{sneath}{AP} = '0.533';
${dict}{sneath}{AQ} = '0.356';
${dict}{sneath}{AN} = '0.28';
${dict}{sneath}{AM} = '0.421';
${dict}{sneath}{AT} = '0.417';
${dict}{sneath}{AS} = '0.477';
${dict}{sneath}{AC} = '0.578';
${dict}{sneath}{AE} = '0.159';
${dict}{sneath}{AD} = '0.156';
${dict}{sneath}{AK} = '0.426';
${dict}{sneath}{AR} = '0.315';
${dict}{sneath}{AY} = '0.214';
${dict}{sneath}{AF} = '0.356';
${dict}{sneath}{AW} = '0.224';
${dict}{sneath}{AH} = '0.32';
${dict}{sneath}{PQ} = '0.168';
${dict}{sneath}{PN} = '0.172';
${dict}{sneath}{PM} = '0.265';
${dict}{sneath}{PT} = '0.330';
${dict}{sneath}{PS} = '0.321';
${dict}{sneath}{PC} = '0.318';
${dict}{sneath}{PE} = '0.003';
${dict}{sneath}{PD} = '0.015';
${dict}{sneath}{PK} = '0.295';
${dict}{sneath}{PR} = '0.155';
${dict}{sneath}{PY} = '0.179';
${dict}{sneath}{PF} = '0.282';
${dict}{sneath}{PW} = '0.211';
${dict}{sneath}{PH} = '0.172';
${dict}{sneath}{QN} = '0.589';
${dict}{sneath}{QM} = '0.699';
${dict}{sneath}{QT} = '0.340';
${dict}{sneath}{QS} = '0.501';
${dict}{sneath}{QC} = '0.482';
${dict}{sneath}{QE} = '0.685';
${dict}{sneath}{QD} = '0.492';
${dict}{sneath}{QK} = '0.545';
${dict}{sneath}{QR} = '0.561';
${dict}{sneath}{QY} = '0.368';
${dict}{sneath}{QF} = '0.459';
${dict}{sneath}{QW} = '0.353';
${dict}{sneath}{QH} = '0.406';
${dict}{sneath}{NM} = '0.518';
${dict}{sneath}{NT} = '0.488';
${dict}{sneath}{NS} = '0.581';
${dict}{sneath}{NC} = '0.485';
${dict}{sneath}{NE} = '0.578';
${dict}{sneath}{ND} = '0.637';
${dict}{sneath}{NK} = '0.401';
${dict}{sneath}{NR} = '0.427';
${dict}{sneath}{NY} = '0.391';
${dict}{sneath}{NF} = '0.34';
${dict}{sneath}{NW} = '0.316';
${dict}{sneath}{NH} = '0.459';
${dict}{sneath}{MT} = '0.409';
${dict}{sneath}{MS} = '0.48';
${dict}{sneath}{MC} = '0.612';
${dict}{sneath}{ME} = '0.402';
${dict}{sneath}{MD} = '0.292';
${dict}{sneath}{MK} = '0.482';
${dict}{sneath}{MR} = '0.522';
${dict}{sneath}{MY} = '0.307';
${dict}{sneath}{MF} = '0.465';
${dict}{sneath}{MW} = '0.355';
${dict}{sneath}{MH} = '0.345';
${dict}{sneath}{TS} = '0.668';
${dict}{sneath}{TC} = '0.485';
${dict}{sneath}{TE} = '0.218';
${dict}{sneath}{TD} = '0.254';
${dict}{sneath}{TK} = '0.224';
${dict}{sneath}{TR} = '0.258';
${dict}{sneath}{TY} = '0.285';
${dict}{sneath}{TF} = '0.254';
${dict}{sneath}{TW} = '0.176';
${dict}{sneath}{TH} = '0.208';
${dict}{sneath}{SC} = '0.613';
${dict}{sneath}{SE} = '0.312';
${dict}{sneath}{SD} = '0.330';
${dict}{sneath}{SK} = '0.285';
${dict}{sneath}{SR} = '0.317';
${dict}{sneath}{SY} = '0.354';
${dict}{sneath}{SF} = '0.380';
${dict}{sneath}{SW} = '0.243';
${dict}{sneath}{SH} = '0.342';
${dict}{sneath}{CE} = '0.221';
${dict}{sneath}{CD} = '0.243';
${dict}{sneath}{CK} = '0.269';
${dict}{sneath}{CR} = '0.324';
${dict}{sneath}{CY} = '0.223';
${dict}{sneath}{CF} = '0.289';
${dict}{sneath}{CW} = '0.188';
${dict}{sneath}{CH} = '0.288';
${dict}{sneath}{ED} = '0.84';
${dict}{sneath}{EK} = '0.435';
${dict}{sneath}{ER} = '0.382';
${dict}{sneath}{EY} = '0.261';
${dict}{sneath}{EF} = '0.219';
${dict}{sneath}{EW} = '0.086';
${dict}{sneath}{EH} = '0.201';
${dict}{sneath}{DK} = '0.248';
${dict}{sneath}{DR} = '0.236';
${dict}{sneath}{DY} = '0.287';
${dict}{sneath}{DF} = '0.172';
${dict}{sneath}{DW} = '0.028';
${dict}{sneath}{DH} = '0.2';
${dict}{sneath}{KR} = '0.733';
${dict}{sneath}{KY} = '0.285';
${dict}{sneath}{KF} = '0.381';
${dict}{sneath}{KW} = '0.297';
${dict}{sneath}{KH} = '0.421';
${dict}{sneath}{RY} = '0.407';
${dict}{sneath}{RF} = '0.339';
${dict}{sneath}{RW} = '0.288';
${dict}{sneath}{RH} = '0.396';
${dict}{sneath}{YF} = '0.729';
${dict}{sneath}{YW} = '0.565';
${dict}{sneath}{YH} = '0.504';
${dict}{sneath}{FW} = '0.741';
${dict}{sneath}{FH} = '0.605';
${dict}{sneath}{WH} = '0.484';
#-------------------------------------
${dict}{deltaH}{PS} = '2.56';
${dict}{deltaH}{SY} = '2.83';
${dict}{deltaH}{TI} = '2.53';
${dict}{deltaH}{ED} = '0.01';
${dict}{deltaH}{IN} = '2.96';
${dict}{deltaH}{PT} = '2.16';
${dict}{deltaH}{ST} = '0.40';
${dict}{deltaH}{TA} = '0.19';
${dict}{deltaH}{HR} = '0.67';
${dict}{deltaH}{VF} = '0.96';
${dict}{deltaH}{PA} = '1.97';
${dict}{deltaH}{SI} = '2.93';
${dict}{deltaH}{ZQ} = '2.32';
${dict}{deltaH}{HD} = '0.86';
${dict}{deltaH}{VA} = '1.06';
${dict}{deltaH}{PL} = '0.18';
${dict}{deltaH}{SF} = '2.61';
${dict}{deltaH}{LH} = '1.02';
${dict}{deltaH}{HN} = '1.39';
${dict}{deltaH}{VL} = '0.73';
${dict}{deltaH}{PQ} = '2.50';
${dict}{deltaH}{SA} = '0.59';
${dict}{deltaH}{LM} = '1.12';
${dict}{deltaH}{MR} = '0.57';
${dict}{deltaH}{TK} = '1.06';
${dict}{deltaH}{PH} = '1.20';
${dict}{deltaH}{SL} = '2.38';
${dict}{deltaH}{LR} = '1.69';
${dict}{deltaH}{RC} = '0.08';
${dict}{deltaH}{TM} = '0.86';
${dict}{deltaH}{PR} = '1.87';
${dict}{deltaH}{SR} = '0.69';
${dict}{deltaH}{LW} = '0.58';
${dict}{deltaH}{RW} = '2.27';
${dict}{deltaH}{TR} = '0.29';
${dict}{deltaH}{GS} = '0.04';
${dict}{deltaH}{SN} = '0.03';
${dict}{deltaH}{KQ} = '1.40';
${dict}{deltaH}{DN} = '0.53';
${dict}{deltaH}{TN} = '0.44';
${dict}{deltaH}{GV} = '1.69';
${dict}{deltaH}{SC} = '0.61';
${dict}{deltaH}{KE} = '0.95';
${dict}{deltaH}{CW} = '2.35';
${dict}{deltaH}{AE} = '0.08';
${dict}{deltaH}{GA} = '0.63';
${dict}{deltaH}{SW} = '2.96';
${dict}{deltaH}{KM} = '0.20';
${dict}{deltaH}{IV} = '1.28';
${dict}{deltaH}{AD} = '0.09';
${dict}{deltaH}{GE} = '0.55';
${dict}{deltaH}{YF} = '0.22';
${dict}{deltaH}{KR} = '0.77';
${dict}{deltaH}{IF} = '0.32';
${dict}{deltaH}{VE} = '1.14';
${dict}{deltaH}{GR} = '0.73';
${dict}{deltaH}{YH} = '1.47';
${dict}{deltaH}{KN} = '1.49';
${dict}{deltaH}{IL} = '0.55';
${dict}{deltaH}{VM} = '0.39';
${dict}{deltaH}{GD} = '0.54';
${dict}{deltaH}{YD} = '2.33';
${dict}{deltaH}{QE} = '0.45';
${dict}{deltaH}{IK} = '1.47';
${dict}{deltaH}{VD} = '1.15';
${dict}{deltaH}{GC} = '0.65';
${dict}{deltaH}{YN} = '2.86';
${dict}{deltaH}{QH} = '1.30';
${dict}{deltaH}{IM} = '1.67';
${dict}{deltaH}{FL} = '0.23';
${dict}{deltaH}{GW} = '3.00';
${dict}{deltaH}{YC} = '2.22';
${dict}{deltaH}{QR} = '0.63';
${dict}{deltaH}{YR} = '2.24';
${dict}{deltaH}{FC} = '2.00';
#------------------------------------
${dict}{codon}{TCA} = 'Ser'; # Serine
${dict}{codon}{TCC} = 'Ser'; # Serine
${dict}{codon}{TCG} = 'Ser'; # Serine
${dict}{codon}{TCT} = 'Ser'; # Serine
${dict}{codon}{TTC} = 'Phe'; # Phenylalanine
${dict}{codon}{TTT} = 'Phe'; # Phenylalanine
${dict}{codon}{TTA} = 'Leu'; # Leucineзамена кодонов
${dict}{codon}{TTG} = 'Leu'; # Leucine
${dict}{codon}{TAC} = 'Tyr'; # Tyrosine
${dict}{codon}{TAT} = 'Tyr'; # Tyrosine
${dict}{codon}{TAA} = 'STOP'; # Ochre
${dict}{codon}{TAG} = 'STOP'; # Amber
${dict}{codon}{TGC} = 'Cys'; # Cysteine
${dict}{codon}{TGT} = 'Cys'; # Cysteine
${dict}{codon}{TGA} = 'STOP'; # Opal
${dict}{codon}{TGG} = 'Trp'; # Tryptophan
${dict}{codon}{CTA} = 'Leu'; # Leucine
${dict}{codon}{CTC} = 'Leu'; # Leucine
${dict}{codon}{CTG} = 'Leu'; # Leucine
${dict}{codon}{CTT} = 'Leu'; # Leucine
${dict}{codon}{CCA} = 'Pro'; # Proline
${dict}{codon}{CCC} = 'Pro'; # Proline
${dict}{codon}{CCG} = 'Pro'; # Proline
${dict}{codon}{CCT} = 'Pro'; # Proline
${dict}{codon}{CAC} = 'His'; # Histidine
${dict}{codon}{CAT} = 'His'; # Histidine
${dict}{codon}{CAA} = 'Gln'; # Glutamine
${dict}{codon}{CAG} = 'Gln'; # Glutamine
${dict}{codon}{CGA} = 'Arg'; # Arginine
${dict}{codon}{CGC} = 'Arg'; # Arginine
${dict}{codon}{CGG} = 'Arg'; # Arginine
${dict}{codon}{CGT} = 'Arg'; # Arginine
${dict}{codon}{ATA} = 'Ile'; # Isoleucine
${dict}{codon}{ATC} = 'Ile'; # Isoleucine
${dict}{codon}{ATT} = 'Ile'; # Isoleucine
${dict}{codon}{ATG} = 'Met'; # Methionine
${dict}{codon}{ACA} = 'Thr'; # Threonine
${dict}{codon}{ACC} = 'Thr'; # Threonine
${dict}{codon}{ACG} = 'Thr'; # Threonine
${dict}{codon}{ACT} = 'Thr'; # Threonine
${dict}{codon}{AAC} = 'Asn'; # Asparagine
${dict}{codon}{AAT} = 'Asn'; # Asparagine
${dict}{codon}{AAA} = 'Lys'; # Lysine
${dict}{codon}{AAG} = 'Lys'; # Lysine
${dict}{codon}{AGC} = 'Ser'; # Serine
${dict}{codon}{AGT} = 'Ser'; # Serine
${dict}{codon}{AGA} = 'Arg'; # Arginine
${dict}{codon}{AGG} = 'Arg'; # Arginine
${dict}{codon}{GTA} = 'Val'; # Valine
${dict}{codon}{GTC} = 'Val'; # Valine
${dict}{codon}{GTG} = 'Val'; # Valine
${dict}{codon}{GTT} = 'Val'; # Valine
${dict}{codon}{GCA} = 'Ala'; # Alanine
${dict}{codon}{GCC} = 'Ala'; # Alanine
${dict}{codon}{GCG} = 'Ala'; # Alanine
${dict}{codon}{GCT} = 'Ala'; # Alanine
${dict}{codon}{GAC} = 'Asp'; # Aspartic Acid
${dict}{codon}{GAT} = 'Asp'; # Aspartic Acid
${dict}{codon}{GAA} = 'Glu'; # Glutamic Acid
${dict}{codon}{GAG} = 'Glu'; # Glutamic Acid
${dict}{codon}{GGA} = 'Gly'; # Glycine
${dict}{codon}{GGC} = 'Gly'; # Glycine
${dict}{codon}{GGG} = 'Gly'; # Glycine
${dict}{codon}{GGT} = 'Gly'; # Glycine
#------------------------------------
${dict}{aa}{Gly} = 'G';
${dict}{aa}{Leu} = 'L';
${dict}{aa}{Tyr} = 'Y';
${dict}{aa}{Ser} = 'S';
${dict}{aa}{Glu} = 'E';
${dict}{aa}{Gln} = 'Q';
${dict}{aa}{Asp} = 'D';
${dict}{aa}{Asn} = 'N';
${dict}{aa}{Phe} = 'F';
${dict}{aa}{Ala} = 'A';
${dict}{aa}{Lys} = 'K';
${dict}{aa}{Arg} = 'R';
${dict}{aa}{His} = 'H';
${dict}{aa}{Cys} = 'C';
${dict}{aa}{Val} = 'V';
${dict}{aa}{Pro} = 'P';
${dict}{aa}{Trp} = 'W';
${dict}{aa}{Ile} = 'I';
${dict}{aa}{Met} = 'M';
${dict}{aa}{Thr} = 'T';
#------------------------------------
${dict}{aa_mw}{Ala} = '71.0788';
${dict}{aa_mw}{Arg} = '156.1875';
${dict}{aa_mw}{Asn} = '114.1038';
${dict}{aa_mw}{Asp} = '115.0886';
${dict}{aa_mw}{Cys} = '103.1388';
${dict}{aa_mw}{Glu} = '129.1155';
${dict}{aa_mw}{Gln} = '128.1307';
${dict}{aa_mw}{Gly} = '57.0519';
${dict}{aa_mw}{His} = '137.1411';
${dict}{aa_mw}{Ile} = '113.1594';
${dict}{aa_mw}{Leu} = '113.1594';
${dict}{aa_mw}{Lys} = '128.1741';
${dict}{aa_mw}{Met} = '131.1926';
${dict}{aa_mw}{Phe} = '147.1766';
${dict}{aa_mw}{Pro} = '97.1167';
${dict}{aa_mw}{Ser} = '87.0782';
${dict}{aa_mw}{Thr} = '101.1051';
${dict}{aa_mw}{Trp} = '186.2132';
${dict}{aa_mw}{Tyr} = '163.1760';
${dict}{aa_mw}{Val} = '99.1326';
#------------------------------------
my @grantham_matrix = qw/
0 112 111 126 195 91 107 60 86 94 96 106 84 113 27 99 58 148 112 64
112 0 86 96 180 43 54 125 29 97 102 26 91 97 103 110 71 101 77 96
111 86 0 23 139 46 42 80 68 149 153 94 142 158 91 46 65 174 143 133
126 96 23 0 154 61 45 94 81 168 172 101 160 177 108 65 85 181 160 152
195 180 139 154 0 154 170 159 174 198 198 202 196 205 169 112 149 215 194 192
91 43 46 61 154 0 29 87 24 109 113 53 101 116 76 68 42 130 99 96
107 54 42 45 170 29 0 98 40 134 138 56 126 140 93 80 65 152 122 121
60 125 80 94 159 87 98 0 98 135 138 127 127 153 42 56 59 184 147 109
86 29 68 81 174 24 40 98 0 94 99 32 87 100 77 89 47 115 83 84
94 97 149 168 198 109 134 135 94 0 5 102 10 21 95 142 89 61 33 29
96 102 153 172 198 113 138 138 99 5 0 107 15 22 98 145 92 61 36 32
106 26 94 101 202 53 56 127 32 102 107 0 95 102 103 121 78 110 85 97
84 91 142 160 196 101 126 127 87 10 15 95 0 28 87 135 81 67 36 21
113 97 158 177 205 116 140 153 100 21 22 102 28 0 114 155 103 40 22 50
27 103 91 108 169 76 93 42 77 95 98 103 87 114 0 74 38 147 110 68
99 110 46 65 112 68 80 56 89 142 145 121 135 155 74 0 58 177 144 124
58 71 65 85 149 42 65 59 47 89 92 78 81 103 38 58 0 128 92 69
148 101 174 181 215 130 152 184 115 61 61 110 67 40 147 177 128 0 37 88
112 77 143 160 194 99 122 147 83 33 36 85 36 22 110 144 92 37 0 55
64 96 133 152 192 96 121 109 84 29 32 97 21 50 68 124 69 88 55 0
/;
my @GD_AAs = qw/A R N D C Q E G H I L K M F P S T W Y V/;
# my %GD_dic;
my $GD_num = @GD_AAs;
for ( my $i = 0; $i < $GD_num; $i++ ) {
for ( my $j = 0; $j < $GD_num; $j++ ) {
# $GD_dic->{GD}->{ $GD_AAs[$i] }->{ $GD_AAs[$j] }
# = $grantham_matrix[ ( $i * $GD_num ) + $j ];
${dict}{GD}->{ $GD_AAs[$i] }->{ $GD_AAs[$j] }
= $grantham_matrix[ ( $i * $GD_num ) + $j ];
}
}
my @blosum45_matrix = qw/
5 -2 -1 -2 -1 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -2 -2 0 -1 -1 0 -5
-2 7 0 -1 -3 1 0 -2 0 -3 -2 3 -1 -2 -2 -1 -1 -2 -1 -2 -1 0 -1 -5
-1 0 6 2 -2 0 0 0 1 -2 -3 0 -2 -2 -2 1 0 -4 -2 -3 4 0 -1 -5
-2 -1 2 7 -3 0 2 -1 0 -4 -3 0 -3 -4 -1 0 -1 -4 -2 -3 5 1 -1 -5
-1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -3 -2 -5
-1 1 0 0 -3 6 2 -2 1 -2 -2 1 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5
-1 0 0 2 -3 2 6 -2 0 -3 -2 1 -2 -3 0 0 -1 -3 -2 -3 1 4 -1 -5
0 -2 0 -1 -3 -2 -2 7 -2 -4 -3 -2 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -5
-2 0 1 0 -3 1 0 -2 10 -3 -2 -1 0 -2 -2 -1 -2 -3 2 -3 0 0 -1 -5
-1 -3 -2 -4 -3 -2 -3 -4 -3 5 2 -3 2 0 -2 -2 -1 -2 0 3 -3 -3 -1 -5
-1 -2 -3 -3 -2 -2 -2 -3 -2 2 5 -3 2 1 -3 -3 -1 -2 0 1 -3 -2 -1 -5
-1 3 0 0 -3 1 1 -2 -1 -3 -3 5 -1 -3 -1 -1 -1 -2 -1 -2 0 1 -1 -5
-1 -1 -2 -3 -2 0 -2 -2 0 2 2 -1 6 0 -2 -2 -1 -2 0 1 -2 -1 -1 -5
-2 -2 -2 -4 -2 -4 -3 -3 -2 0 1 -3 0 8 -3 -2 -1 1 3 0 -3 -3 -1 -5
-1 -2 -2 -1 -4 -1 0 -2 -2 -2 -3 -1 -2 -3 9 -1 -1 -3 -3 -3 -2 -1 -1 -5
1 -1 1 0 -1 0 0 0 -1 -2 -3 -1 -2 -2 -1 4 2 -4 -2 -1 0 0 0 -5
0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 2 5 -3 -1 0 0 -1 0 -5
-2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2 1 -3 -4 -3 15 3 -3 -4 -2 -2 -5
-2 -1 -2 -2 -3 -1 -2 -3 2 0 0 -1 0 3 -3 -2 -1 3 8 -1 -2 -2 -1 -5
0 -2 -3 -3 -1 -3 -3 -3 -3 3 1 -2 1 0 -3 -1 0 -3 -1 5 -3 -3 -1 -5
-1 -1 4 5 -2 0 1 -1 0 -3 -3 0 -2 -3 -2 0 0 -4 -2 -3 4 2 -1 -5
-1 0 0 1 -3 4 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -3 2 4 -1 -5
0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 -2 -1 -1 -1 -1 -1 -5
-5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1
/;
my @B45_AAs = qw/A R N D C Q E G H I L K M F P S T W Y V B Z X */;
# my %GD_dic;
my $B45_num = @B45_AAs;
for ( my $i = 0; $i < $B45_num; $i++ ) {
for ( my $j = 0; $j < $B45_num; $j++ ) {
# $GD_dic->{GD}->{ $GD_AAs[$i] }->{ $GD_AAs[$j] }
# = $grantham_matrix[ ( $i * $GD_num ) + $j ];
${dict}{B45}->{ $B45_AAs[$i] }->{ $B45_AAs[$j] }
= $blosum45_matrix[ ( $i * $B45_num ) + $j ];
}
}
my @pam30_matrix = qw/
6 -7 -4 -3 -6 -4 -2 -2 -7 -5 -6 -7 -5 -8 -2 0 -1 -13 -8 -2 -3 -3 -3 -17
-7 8 -6 -10 -8 -2 -9 -9 -2 -5 -8 0 -4 -9 -4 -3 -6 -2 -10 -8 -7 -4 -6 -17
-4 -6 8 2 -11 -3 -2 -3 0 -5 -7 -1 -9 -9 -6 0 -2 -8 -4 -8 6 -3 -3 -17
-3 -10 2 8 -14 -2 2 -3 -4 -7 -12 -4 -11 -15 -8 -4 -5 -15 -11 -8 6 1 -5 -17
-6 -8 -11 -14 10 -14 -14 -9 -7 -6 -15 -14 -13 -13 -8 -3 -8 -15 -4 -6 -12 -14 -9 -17
-4 -2 -3 -2 -14 8 1 -7 1 -8 -5 -3 -4 -13 -3 -5 -5 -13 -12 -7 -3 6 -5 -17
-2 -9 -2 2 -14 1 8 -4 -5 -5 -9 -4 -7 -14 -5 -4 -6 -17 -8 -6 1 6 -5 -17
-2 -9 -3 -3 -9 -7 -4 6 -9 -11 -10 -7 -8 -9 -6 -2 -6 -15 -14 -5 -3 -5 -5 -17
-7 -2 0 -4 -7 1 -5 -9 9 -9 -6 -6 -10 -6 -4 -6 -7 -7 -3 -6 -1 -1 -5 -17
-5 -5 -5 -7 -6 -8 -5 -11 -9 8 -1 -6 -1 -2 -8 -7 -2 -14 -6 2 -6 -6 -5 -17
-6 -8 -7 -12 -15 -5 -9 -10 -6 -1 7 -8 1 -3 -7 -8 -7 -6 -7 -2 -9 -7 -6 -17
-7 0 -1 -4 -14 -3 -4 -7 -6 -6 -8 7 -2 -14 -6 -4 -3 -12 -9 -9 -2 -4 -5 -17
-5 -4 -9 -11 -13 -4 -7 -8 -10 -1 1 -2 11 -4 -8 -5 -4 -13 -11 -1 -10 -5 -5 -17
-8 -9 -9 -15 -13 -13 -14 -9 -6 -2 -3 -14 -4 9 -10 -6 -9 -4 2 -8 -10 -13 -8 -17
-2 -4 -6 -8 -8 -3 -5 -6 -4 -8 -7 -6 -8 -10 8 -2 -4 -14 -13 -6 -7 -4 -5 -17
0 -3 0 -4 -3 -5 -4 -2 -6 -7 -8 -4 -5 -6 -2 6 0 -5 -7 -6 -1 -5 -3 -17
-1 -6 -2 -5 -8 -5 -6 -6 -7 -2 -7 -3 -4 -9 -4 0 7 -13 -6 -3 -3 -6 -4 -17
-13 -2 -8 -15 -15 -13 -17 -15 -7 -14 -6 -12 -13 -4 -14 -5 -13 13 -5 -15 -10 -14 -11 -17
-8 -10 -4 -11 -4 -12 -8 -14 -3 -6 -7 -9 -11 2 -13 -7 -6 -5 10 -7 -6 -9 -7 -17
-2 -8 -8 -8 -6 -7 -6 -5 -6 2 -2 -9 -1 -8 -6 -6 -3 -15 -7 7 -8 -6 -5 -17
-3 -7 6 6 -12 -3 1 -3 -1 -6 -9 -2 -10 -10 -7 -1 -3 -10 -6 -8 6 0 -5 -17
-3 -4 -3 1 -14 6 6 -5 -1 -6 -7 -4 -5 -13 -4 -5 -6 -14 -9 -6 0 6 -5 -17
-3 -6 -3 -5 -9 -5 -5 -5 -5 -5 -6 -5 -5 -8 -5 -3 -4 -11 -7 -5 -5 -5 -5 -17
-17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 -17 1
/;
# print "@pam30_matrix\n";
my @PAM30_AAs = qw/A R N D C Q E G H I L K M F P S T W Y V B Z X */;
# print "@PAM30_AAs\n";
my $PAM30_num = @PAM30_AAs;
for ( my $i = 0; $i < $PAM30_num; $i++ ) {
for ( my $j = 0; $j < $PAM30_num; $j++ ) {
${dict}{PAM30}->{ $PAM30_AAs[$i] }->{ $PAM30_AAs[$j] }
= $pam30_matrix[ ( $i * $PAM30_num ) + $j ];
}
}
# $annotations{$locus_tag}{nucleotide} = $nucleotide;
$gene = undef;
$locus_tag = undef;
$gene_synonym = undef;
$protein_id = undef;
}
}
# $annotations{options}{genome_seq} = $genome_seq;
$annotations{options}{version} = $version;
# $annotations{options}{logo} = $logo;
$annotations{options}{reference} = $display_id;
$annotations{options}{strain_name} = $strain_name;
$annotations{options}{organism_name} = $organism_name;
print "Genome length: $genome_length bp\n";
print "Reference id: $display_id\n";
#-----------------------------------------------
if ( $snp_list ne "" ) {
my $loc_snp_count = 0;
my ( $col1, $col2, $col3, $col4 );
my $snp_list_name = "";
my $snp_notation = "";
$annotations{options}{snp_list_exists} = 1;
open( my $fh, "<", $snp_list )
or die "cannot open < $snp_list: $!";
while (<$fh>) {
next if substr( $_, 0, 1 ) eq "#";
my $str = "$_";
chomp($str);
( $col1, $col2, $col3, $col4 ) = split( "\t", $str );
# print "$snp_list_name\n$col2\t$col3\n";
# push(@snp_list_a,$)
$snp_list_name = $col1 if ( $col1 ne "" );
next if ( $col2 eq "" );
if ( $snp_list_name ne ""
&& $col3 ne ""
&& $col4 ne "" )
{
$snp_notation = check_snp_notation($col3);
# print "$snp_notation\t$col3\t$col4\n";
if ( $snp_notation eq "nc_gene" && $col2 ne "" ) {
${dict}{snp_list}{coding}{$snp_list_name}{ uc($col2) }
{ uc($col3) }{'note'} = $col4;
}
elsif ( $snp_notation eq "nc_genome" ) {
${dict}{snp_list}{coding}{$snp_list_name}{ uc($col3) }
{'note'} = $col4;
}
elsif ( $snp_notation eq "pos" ) {
# my ($pos_val)=$col3=~/(\d+)/;
${dict}{snp_list}{coding}{$snp_list_name}{ uc($col3) }
{'note'} = $col4;
# print "$snp_list_name\t$col3\t$col4\t$pos_val\n";
}
elsif ( $snp_notation eq "codon" ) {
# my ($pos_val)=$col3=~/(\d+)/;
${dict}{snp_list}{coding}{$snp_list_name}{ uc($col2) }
{ uc($col3) }{'note'} = $col4;
}
elsif ( $snp_notation eq "igpos" ) {
# my ($pos_val)=$col3=~/(\d+)/;
${dict}{snp_list}{intergenic}{$snp_list_name}
{ uc($col3) }{'note'} = $col4;
$annotations{options}{igpos_list_exists} = 1;
}
elsif ( $snp_notation eq "aa_genome" ) {
${dict}{snp_list}{coding}{$snp_list_name}{ uc($col3) }
{'note'} = $col4;
}
elsif ( $snp_notation eq "aa_genome_long" ) {
${dict}{snp_list}{coding}{$snp_list_name}{ uc($col3) }
{'note'} = $col4;
}
elsif ( $snp_notation eq "aa" && $col2 ne "" ) {
${dict}{snp_list}{coding}{$snp_list_name}{ uc($col2) }
{ uc($col3) }{'note'} = $col4;
}
elsif ( $snp_notation eq "aa_long" ) {
${dict}{snp_list}{coding}{$snp_list_name}{ uc($col2) }
{ uc($col3) }{'note'} = $col4;
}
$loc_snp_count++;
}
else {
print "Bad format of $snp_list file!\n";
$annotations{options}{snp_list_exists} = 0;
$annotations{options}{igpos_list_exists} = 0;
}
# $str =~ /^(\w+)\t(\S+)\t(.*)/;
# if ( $col1 eq "" ) {
# print "Bad format of $snp_list file!\n";
# $annotations{options}{snp_list_exists} = 0;
# }
# else {
# ${dict}{snp_list}{ uc($col2) . "_" . uc($col3) }{'note'} = $col4;
# $loc_snp_count++;
# # last;
# }
# my $loc_pos=$1;
# my $loc_ref=$2;
# my $loc_alt=$3;
}
close $fh;
print "SNP's processed: $loc_snp_count\n";
}
else {
$annotations{options}{snp_list_exists} = 0;
print "SNP's processed: file not set\n";
}
#-----------------------------------------------
# $annotations{options}{codon_usage} = "no";
my %hoh = ( annotations => \%annotations, dict => \%dict );
# store \%hoh, 'HoH.sto';
print "CDS processed: $count_genes\n";
print "Filename: $out_file\n";
print "Version: $version\n";
print "-" x 50 . "\n";
my $tmp_annotations = freeze( \%hoh );
# my $tmp_tang=
my $buffer = "";
my $fh = tempfile();
open $fh, '>', \$buffer;
print $fh $tmp_annotations;
# print $fh $tmp_annotations;
rawdeflate \$buffer => $out_file
or die "rawdeflate failed: $RawDeflateError\n";
}
# sub codon_usage_db {
# my $loc_read_file = "";
# open( FILE, $codon_usage )
# or die "Couldn't open file $codon_usage, $!"
# # ; #открываем каждый файл
# while (<FILE>) { # ищем строки со снипами
# $loc_read_file =~ /locus_tag="(\w+)".*\n(.*)/;
# print "$loc_read_file\n";
# }
# # body...
# }
# @read_codon_info="";
# if ($codon_file) {