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getSequenceInfo.pl
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#!/usr/bin/perl
################################################################################
## "Copyright 2019 Vincent Moco and David Couvin"
## licence GPL-3.0-or-later
## This program is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at your option) any later version.
## This program is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
## You should have received a copy of the GNU General Public License
## along with this program. If not, see <https://www.gnu.org/licenses/>.
################################################################################
use strict;
use warnings;
my $version = "1.0.1"; # version
# Date and time of the current day (Beginning)
my ($start_year,$start_month,$start_day, $start_hour,$start_min,$start_sec) = Today_and_Now();
print "##################################################################\n";
print "## ---> Welcome to $0 (version $version)!\n";
print "## Start Date (yyyy-mm-dd, hh:min:sec): $start_year-$start_month-$start_day, $start_hour:$start_min:$start_sec\n";
print "##################################################################\n\n";
#BioPerl has been removed from the @modules
my @modules = qw(
Archive::Tar
Bio::SeqIO
Bio::Species
Date::Calc
File::Copy
File::Path
Net::FTP
IO::Uncompress::Gunzip
LWP::Simple
POSIX
File::Log
);
foreach my $module (@modules) {
if (isModuleInstalled($module)) {
print "$module is.................installed!\n";
}
else {
print "$module is not installed. Please install it and try again.\n";
print "You can reinstall the $0 as shown on the README page or use the following command to install the module:\n";
print "cpan -i -f $module\n";
#system("cpan -i -f $module");
exit 1;
}
}
print "\n";
use Archive::Tar;
use Bio::SeqIO;
use Bio::Species;
use Date::Calc qw(:all);
use File::Copy qw(cp move);
use File::Path qw(rmtree);
use Net::FTP;
use IO::Uncompress::Gunzip qw(gunzip $GunzipError);
use LWP::Simple qw(get);
use POSIX qw(floor);
use File::Log;
####################################################################################################
## A Perl script allowing to get sequence information from GenBank, RefSeq or ENA repositories.
##
####################################################################################################
### main program
### parameters
my $directory = "genbank";
my $kingdom = ""; # kingdom of organism
my $releaseDate = "0000-00-00"; # sequences are downloaded from this release date
my $components; # components of the assembly
my $species = ""; # species name
my $getSummaries; # indicates if a new assembly summary is required
my $assemblyLevel = "Complete Genome,Chromosome,Scaffold,Contig"; # assembly level of the genome
my $quantity; # limit number of assemblies to download
my $sequenceID;
my $ftpServor = "ftp.ncbi.nlm.nih.gov";
my $enaFtpServor = "ftp.sra.ebi.ac.uk";
my $fldSep = "/"; # folder seperation change by OS
my @availableKingdoms = (
"archaea",
"bacteria",
"fungi",
"invertebrate",
"plant",
"protozoa",
"vertebrate_mammalian",
"vertebrate_other",
"viral"
); # list of available kingdoms
my $actualOS = "Unix"; # OS of the computer
my $mainFolder; # folder in which the assemblies results are stored
my $assemblyTaxid = ""; # taxid for assembly
my $sraID; # SRA sequence ID
my $assemblyPrjID; # assembly or prj ID
my $log; # log
if (@ARGV<1) {
help_user_simple($0);
exit 1;
}
if ($ARGV[0] eq "-help" || $ARGV[0] eq "-h") {
help_user_advance($0);
exit 0;
}
if ($ARGV[0] eq "-version" || $ARGV[0] eq "-v") {
program_version($0);
exit 0;
}
##requirements
for (my $i = 0; $i <= $#ARGV; $i++) {
if ($ARGV[$i]=~/-kingdom/i or $ARGV[$i]=~/-k/i) {
$kingdom = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/-directory/i or $ARGV[$i]=~/-dir/i) {
$directory = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/-date/i) {
$releaseDate = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/-getSummaries/i or $ARGV[$i]=~/-get/i) {
$getSummaries = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/-species/i or $ARGV[$i]=~/-s/i) {
$species = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/-level/i or $ARGV[$i]=~/-le/i) {
$assemblyLevel = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/-components/i or $ARGV[$i]=~/-c/i) {
$components = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/-quantity/i or $ARGV[$i]=~/-q/i or $ARGV[$i]=~/-number/i or $ARGV[$i]=~/-n/i) {
$quantity = int($ARGV[$i+1]);
}
elsif ($ARGV[$i]=~/-ena/i) {
$sequenceID = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/-output/i or $ARGV[$i]=~/-o/i) {
$mainFolder = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/-taxid/i) {
$assemblyTaxid = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/-fastq/i) {
$sraID = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/-assembly_or_project/i) {
$assemblyPrjID = $ARGV[$i+1];
}
elsif ($ARGV[$i]=~/-log/i) {
$log = File::Log->new({
debug => 4,
logFileName => 'myLogFile.log',
logFileMode => '>',
dateTimeStamp => 1,
stderrRedirect => 1,
defaultFile => 0,
logFileDateTime => 1,
appName => 'getSequenceInfo',
PIDstamp => 0,
storeExpText => 1,
msgprepend => '',
say => 1,
});
}
}
#define folcer separator and OS
if ($^O =~ /MSWin32/) {
$fldSep = "\\";
$actualOS = "MSWin32";
}
print "Working ...\n";
if ($kingdom eq "viruses") { $kingdom = "viral"; }
if (grep(/^$kingdom$/i, @availableKingdoms)) {
my @patternParametersList;
my @levelList = split /,/, $assemblyLevel;
if ($species ne "") {
my @speciesList = split(/,/, $species);
foreach my $actualSpecies (@speciesList) {
get_assembly_summary_species( $quantity, $releaseDate, $directory,$kingdom, $actualSpecies,
\@levelList, $fldSep, $actualOS, $mainFolder, $assemblyTaxid, $log,
$getSummaries, $components, $ftpServor);
}
}
elsif ($assemblyTaxid ne "") {
my @taxidList = split(/,/, $assemblyTaxid);
foreach my $actualID (@taxidList) {
get_assembly_summary_species($quantity, $releaseDate, $directory,$kingdom,$species,
\@levelList, $fldSep, $actualOS, $mainFolder, $actualID, $log,
$getSummaries, $components, $ftpServor);
}
}
else {
get_assembly_summary_species($quantity, $releaseDate, $directory,$kingdom,$species,
\@levelList, $fldSep, $actualOS, $mainFolder, $assemblyTaxid, $log,
$getSummaries, $components, $ftpServor);
}
}
if ($sequenceID) {
my @sequenceIDList = split /,/, $sequenceID;
foreach my $enaID (@sequenceIDList) {
sequence_ena($enaID, $log);
}
}
if ($sraID) {
my @sraIDList = split /,/, $sraID;
foreach my $sra (@sraIDList) {
download_ena_fastq($enaFtpServor, $sra, $log);
}
}
if ($assemblyPrjID) {
download_assembly_or_project($assemblyPrjID, $ftpServor, $fldSep, $directory, $log);
}
my ($end_year,$end_month,$end_day, $end_hour,$end_min,$end_sec) = Today_and_Now();
my ($D_y,$D_m,$D_d, $Dh,$Dm,$Ds) =
Delta_YMDHMS($start_year,$start_month,$start_day, $start_hour, $start_min, $start_sec,
$end_year, $end_month, $end_day, $end_hour,$end_min,$end_sec);
print "End Date: $end_year-$end_month-$end_day, $end_hour:$end_min:$end_sec\n";
print "Thank you for using getSequenceInfo!\n";
print "Execution time: $D_y years, $D_m months, $D_d days, $Dh:$Dm:$Ds (hours:minutes:seconds)\n";
### subroutine
# display global help document
sub help_user_simple {
my $programme = shift @_;
print STDERR "Usage : perl $programme [options] \n";
print "Type perl $programme -version or perl $programme -v to get the current version\n";
print "Type perl $programme -help or perl $programme -h to get full help\n";
}
#------------------------------------------------------------------------------
# display full help document
sub help_user_advance {
print <<HEREDOC;
Name:
$0
Synopsis:
A Perl script allowing to get sequence information from GenBank RefSeq or ENA repositories.
Usage:
perl $0 [options]
examples:
perl $0 -k bacteria -s "Helicobacter pylori" -l "Complete Genome" -date 2019-06-01
perl $0 -k viruses -n 5 -date 2019-06-01
perl $0 -k "bacteria" -taxid 9,24 -n 10 -c plasmid -dir genbank -o Results
perl $0 -ena BN000065
perl $0 -fastq ERR818002
perl $0 -fastq ERR818002,ERR818004
Kingdoms:
archaea
bacteria
fungi
invertebrate
plant
protozoa
vertebrate_mammalian
vertebrate_other
viral
Assembly levels:
"Complete Genome"
Chromosome
Scaffold
Contig
General:
-help or -h displays this help
-version or -v displays the current version of the program
Options ([XXX] represents the expected value):
-directory or -dir [XXX] allows to indicate the NCBI's nucleotide sequences repository (default: $directory)
-get or -getSummaries [XXX] allows to obtain a new assembly summary file in function of given kingdoms (bacteria,fungi,protozoa...)
-k or -kingdom [XXX] allows to indicate kingdom of the organism (see the examples above)
-s or -species [XXX] allows to indicate the species (must be combined with -k option)
-taxid [XXX] allows to indicate a specific taxid (must be combined with -k option)
-assembly_or_project [XXX] allows to indicate a specific assembly accession or bioproject (must be combined with -k option)
-date [XXX] indicates the release date (with format yyyy-mm-dd) from which sequence information are available
-l or -level [XXX] allows to select a specific assembly level (e.g. "Complete Genome")
-o or -output [XXX] allows users to name the output result folder
-n or -number [XXX] allows to limit the total number of assemblies to be downloaded
-c or -components [XXX] allows to select specific components of the assembly (e.g. plasmid, chromosome, ...)
-ena [XXX] allows to download report and fasta file given a ENA sequence ID
-fastq [XXX] allows to download FASTQ sequences from ENA given a run accession (https://ena-docs.readthedocs.io/en/latest/faq/archive-generated-files.html)
-log allows to create a log file
HEREDOC
}
#------------------------------------------------------------------------------
# display program version
sub program_version {
my $programme = shift @_;
print "\n $programme, version : $version\n";
print "\n A perl script to get sequences informations\n";
}
#------------------------------------------------------------------------------
sub get_assembly_summary_species {
my ($quantity, $releaseDate, $directory, $kingdom, $species, $levelList, $fldSep,
$actualOS, $mainFolder, $assemblyTaxid, $log, $getSummaries, $components, $ftpServor) = @_;
# assembly_summary.txt file from NCBI FTP site
#my $assemblySummary = get_summaries($ftpServor, $kingdom, $getSummaries, $directory);
my $assemblySummary = download_summaries($directory, $kingdom, $ftpServor, $fldSep, $getSummaries);
#lineage folder
# my $lineage_file = "/pub/taxonomy/new_taxdump/new_taxdump.tar.gz";
# allow to check old summary download
my $oldKingdom = "";
# start of output file
if ($log) {$log->msg(1, "download assembly_summary.txt");}
# if ($actualOS =~ /Unix/i) {
#initialiaze tar manipulation
# my $tar = Archive::Tar->new;
#download taxdump folder
# download_file($ftpServor, $lineage_file);
# $tar->read("new_taxdump.tar.gz");
# $tar->extract_file("rankedlineage.dmp");
# }
my $kingdomRep = $kingdom."_".$start_year."_".$start_month."_".$start_day;
if ($mainFolder) { $kingdomRep = $mainFolder; }
mkdir $kingdomRep unless -d $kingdomRep;
# Repository for request
my $repositoryAssembly = "assembly_repository_".$species."_".$assemblyTaxid."_".$kingdom."_".$start_year."_".$start_month."_".$start_day;
mkdir $repositoryAssembly unless -d $repositoryAssembly;
my $oldAssemblyRep = "." . $fldSep . $kingdomRep . $fldSep . $repositoryAssembly;
if (-d $oldAssemblyRep) { rmtree($oldAssemblyRep) }
# Repository for fna file
my $repositoryFNA = "Assembly";
mkdir $repositoryFNA unless -e $repositoryFNA;
# Repository for genbank file
my $repositoryGenbank = "GenBank";
mkdir $repositoryGenbank unless -e $repositoryGenbank;
# Reposotiry for report file
my $repositoryReport = "Report";
mkdir $repositoryReport unless -e $repositoryReport ;
# Repositories for required components
my %componentsRepHash;
if ($components) {
for my $component (split /,/, $components) {
my $specificRep = $component."_".$species."_".$kingdom."_".$start_year."_".$start_month."_".$start_day;
mkdir $specificRep unless -d $specificRep;
$componentsRepHash{$component} = $specificRep;
}
}
if ($log) {$log->msg(1,"create kingdom and components repository");}
my %assemblyReportList;
my @assemblyRepresentationList = qw/Full Partial/;
my @levelList = @{$levelList};
my $checkCompleteGenome = grep(/complete genome/i, @levelList);
if ($checkCompleteGenome > 0) {@assemblyRepresentationList = qw/Full/;}
if (-e $assemblySummary) {
# Read file
open (SUM, $assemblySummary) or die " error open assembly_summary.txt $!:";
while(<SUM>) {
chomp;
if ($_ !~ m/^#/) {
my @infoList = split /\t/, $_;
my $foundAssemRep = grep (/$infoList[13]/i, @assemblyRepresentationList);
my $checkLevel = grep(/$infoList[11]/i, @levelList);
if ($foundAssemRep > 0 && $checkLevel > 0) {
my $indexInfo = 0;
my $searchPattern = "";
my $regex = "";
if ($species !~ /^$/) {
$indexInfo = 7;
$searchPattern = $species;
$regex = qr/$searchPattern/i;
}
elsif ($assemblyTaxid !~ /^$/) {
$indexInfo = 5;
$searchPattern = $assemblyTaxid;
$regex = qr/^$searchPattern$/i;
}
if (($infoList[$indexInfo] =~ $regex) or ($kingdom !~ /^$/ && $searchPattern =~ /^$/)) {
my @gcfInfo = split(/\//, $infoList[19]);
my $gcfName = pop(@gcfInfo);
my $realDate = $infoList[14];
$realDate =~ s/\//-/g;
my $genbankFile = $infoList[19] . "/" . $gcfName . "_genomic.gbff.gz";
my $dnaFile = $infoList[19] . "/" . $gcfName . "_genomic.fna.gz";
my $assemblyReport = $infoList[19] . "/" . $gcfName . "_assembly_report.txt";
if ($realDate gt $releaseDate) {
$dnaFile = obtain_file($ftpServor, $dnaFile);
$genbankFile = obtain_file($ftpServor, $genbankFile);
$assemblyReport = obtain_file($ftpServor, $assemblyReport);
download_file($ftpServor, $dnaFile);
download_file($ftpServor, $genbankFile);
download_file($ftpServor, $assemblyReport);
if ($log) {$log->msg(1,"download fasta genbank report file");}
# download sequences and check number of "N" characters
my $fileFasta = $gcfName."_genomic.fna.gz";
my $ucpFasta = $gcfName."_genomic.fna";
if (-e $fileFasta) {
gunzip $fileFasta => $ucpFasta or die "gunzip failed: $GunzipError\n";
move($ucpFasta, $repositoryFNA) or die "move failed: $!";
}
if ($log) {$log->msg(1, "unzip fasta file $fileFasta");}
# download genome report
my $fileReport = $gcfName."_assembly_report.txt";
if (-e $fileReport) {
my $fileInformations = $gcfName."_informations.xls";
move($fileReport, $repositoryReport) or die "move failed: $!";
}
# download genbank files
my $fileGenbank = $gcfName."_genomic.gbff.gz";
my $ucpGenbank = $gcfName."_genomic.gbff";
if (-e $fileGenbank) {
gunzip $fileGenbank => $ucpGenbank or die "gunzip failed: $GunzipError\n";
move($ucpGenbank, $repositoryGenbank) or die "move failed: $!";
}
if ($log) {$log->msg(1, "unzip genbank file $fileGenbank");}
# association report and fasta
my $fileFastaGenbank = $ucpFasta . "," . $ucpGenbank;
$assemblyReportList{$fileReport} = $fileFastaGenbank;
if ($quantity) { $quantity -= 1; }
}
}
}
}
if (defined $quantity && $quantity == 0) {
$quantity = undef;
last;
}
}
close(SUM) or die "close file error : $!";
if (!keys %assemblyReportList) {
print "##################################################################\n";
print "No results were found for the following query:\n";
print "perl $0 @ARGV\n";
print "##################################################################\n\n";
if ($actualOS =~ /unix/i) { unlink glob "*.dmp *.gz" or die "for file *.dmp *.gz $!:"; }
if (empty_folder($kingdomRep)) { rmdir $kingdomRep or die "fail remove directory $!:"; }
rmdir $repositoryAssembly or die "failed to remove directory $!:";
rmdir $repositoryFNA or die "failed to remove directory $!:";
rmdir $repositoryGenbank or die "failed to remove directory $!:";
rmdir $repositoryReport or die "failed to remove directory $!:";
if ($components) {
for my $componentRep (values %componentsRepHash) {
rmdir $componentRep or die "failed to remove directory $!:";
}
}
if ($log) {$log->msg(1,"No results were found for the following query:");}
if ($log) {$log->msg(1,"perl $0 @ARGV");}
}
else {
if ($log) {$log->msg(1,"Results were found for the following query:");}
if ($log) {$log->msg(1,"perl $0 @ARGV");}
# write summary files
my %componentsSumHash;
my @keysList = keys %assemblyReportList;
my $summary = "summary.xls";
my $htmlSummary = "summary.html";
if ($components) {
for my $component (split /,/, $components) {
my $specificSummary = $component. "_summary.xls";
$componentsSumHash{$component} = $specificSummary;
}
}
my $fileReport = "." . $fldSep. $repositoryReport . $fldSep . $keysList[0];
my @header = ();
open(FILE, $fileReport) or die "error open file : $!";
while(<FILE>) {
chomp;
if($_ =~ /:/){
$_ =~ s/^#*//;
my @ligne = split /:/, $_;
push(@header, $ligne[0]);
}
}
close(FILE) or die "error close file : $!";
open(HEAD, ">", $summary) or die " error open file : $!";
foreach(@header) {
print HEAD $_ . "\t";
}
print HEAD "Pubmed\tNucleScore\tClassification\t";
print HEAD "Country\tHost\tIsolation source\tA percent\t";
print HEAD "T percent\tG percent\tC percent\tN percent\tGC percent\t";
print HEAD "ATGC ratio\tLength\tShape\n";
close(HEAD) or die "error close file : $!";
if ($components) {
foreach my $componentSummary (values %componentsSumHash) {
open(SUM, ">>", $componentSummary) or die "error open file : $!";
print SUM "Id\tAssembly\tDescription\tLength\tStatus\tLevel\t";
print SUM "GC percent\tA percent\tT percent\tG percent\tC percent\n";
close(SUM) or die "error close file : $!";
}
}
for my $file (@keysList) {
my $reportFile = $repositoryReport . $fldSep . $file;
my @fastaGenbank = split /,/, $assemblyReportList{$file};
my $extFasta = $fastaGenbank[0];
my $extGenbank = $fastaGenbank[1];
my $fnaFile = $repositoryFNA . $fldSep . $extFasta;
my $genbankFile = $repositoryGenbank . $fldSep . $extGenbank;
write_assembly($reportFile, $fnaFile, $genbankFile, $summary, $repositoryAssembly,
\%componentsSumHash, $kingdom, $actualOS, \@header, $log);
if ($log) {$log->msg(1," call write_assembly subroutine");}
}
write_html_summary($summary);
if ($log) {$log->msg(1,"call write_html_summary subroutine");}
if ($components) {
my @componentList = keys %componentsSumHash;
my %componentFastaHash = create_component_sequence_file($fldSep, $repositoryFNA, \@componentList);
if (keys %componentFastaHash && $log) { $log->msg(1,"call create_component_sequence_file subroutine");}
foreach my $component (keys %componentFastaHash) {
move($componentFastaHash{$component}, $componentsRepHash{$component}) or die "move failed: $!";
}
}
move($summary, $repositoryAssembly) or die "move failed: $!";
move($htmlSummary, $repositoryAssembly) or die "move failed: $!";
move($repositoryFNA, $repositoryAssembly . $fldSep . $repositoryFNA) or die "move failed: $!";
move($repositoryGenbank, $repositoryAssembly . $fldSep . $repositoryGenbank) or die "move failed: $!";
move($repositoryReport , $repositoryAssembly . $fldSep . $repositoryReport) or die "move failed: $!";
if ($log) {$log->msg(1, "move fasta, genbank, report to query folder");}
if ($components) {
for my $component (keys %componentsSumHash) {
move($componentsSumHash{$component}, $componentsRepHash{$component}) or die "move failed: $!";
move($componentsRepHash{$component}, $repositoryAssembly . $fldSep . $componentsRepHash{$component}) or die "move failed: $!"
}
if ($log) {$log->msg(1, "move component files to folders");}
}
move($repositoryAssembly, $kingdomRep . $fldSep . $repositoryAssembly) or die "move failed: $!";
if ($log) {$log->msg(1, "move query folder to main folder");}
# if ($actualOS =~ /unix/i) { unlink glob "*.dmp" or die "for file *.dmp $!:"; }
unlink glob "*.gz sequence.txt" or die "$!: for file *.gz sequence.txt";
}
}
}
#write general assembly file
sub write_assembly {
my ($reportFile, $fnaFile, $genbankFile, $summary, $repositoryAssembly,
$componentsSumHashRef, $kingdom, $actualOS, $headerRef, $log) = @_;
my %componentsSumHash = %{$componentsSumHashRef};
my @header = @{$headerRef};
my %hashInformations = ();
my $seq = "";
my $genomeName = "";
my $country = "na";
my $GCpercent = -1;
my $taxId = "na";
my $assemblyLine;
my $pubmedId = "na";
my $host = "na";
my $isoSource = "na";
# my $species = "na";
# my $genus = "na";
# my $family = "na";
# my $order = "na";
# my $class = "na";
# my $phylum = "na";
my $shape = "na";
my $geneNumber = "na";
open(REP, "<", $reportFile) or die "error open file $!:";
while (<REP>) {
chomp;
$_ =~ s/^#*//;
if ($_ =~ /assembled-molecule/i) { $assemblyLine = $_; }
if ($_ =~ /:/) {
my @line = split /:/, $_;
if ($line[1]) { $hashInformations{$line[0]} = trim($line[1]); }
}
}
close(REP) or die "error close file $!:";
open(SUM, ">>", $summary) or die "error open file $!:";
foreach my $k(@header) {
if (grep $_ eq $k, keys %hashInformations) {
my $information = $hashInformations{$k};
if ($k =~ /Assembly name/i) { $genomeName = $information; }
if ($information =~ /^\s*$/) {
print SUM "na\t";
} else {
print SUM $information . "\t";
}
} else {
print SUM "na\t";
}
}
close(SUM) or die "error close file $!:";
open(FNA, "<", $fnaFile) or die "Could not open $!:";
while (<FNA>) {
chomp;
if ($_ !~ /^>/) { $seq .= $_; }
}
close(FNA) or die "error close file :$!";
foreach my $summaryKey (keys %hashInformations) {
if ($summaryKey =~ /taxid/i) {
$taxId = $hashInformations{$summaryKey};
}
}
my $classification = get_taxonomic_rank_genbank($genbankFile);
if ($log) {$log->msg(1, "get taxonomic rank from genbank file");}
$GCpercent = gc_percent($seq);
my ($ade, $thy, $gua, $cyt, $n, $length) = number_nuc_length_seq($fnaFile);
my ($aPercent, $tPercent, $gPercent, $cPercent, $nPercent) = nucleotid_percent($ade, $thy, $gua, $cyt, $n, $length);
my $atgcRatio = atgc_ratio($ade, $thy, $gua, $cyt);
my @percentList = ($aPercent, $tPercent, $gPercent, $cPercent, $nPercent);
my $variance = shift_data_variance(@percentList);
my $nucleScore = nucle_score($variance, $GCpercent, $atgcRatio, $length);
if ($log) {$log->msg(1, "compute GC percent nucleotid percent ATGC ratio NucleScore");}
open(GBFF, "<", $genbankFile) or die "Error open file $!:";
while(<GBFF>) {
chomp;
if ($_ =~ /\/country="(.*)"/) { $country = trim($1); }
if ($_ =~ /PUBMED(.*)/) { $pubmedId = trim($1); }
if ($_ =~ /\/host="(.*)"/) { $host = trim($1); }
if ($_ =~ /\/isolation_source="(.*)"/) { $isoSource = trim($1); }
if ($_ =~ /\(Genes \(total\)\s+::(.*)/) { $geneNumber = trim($1); }
if ($_ =~ /LOCUS.*\s+([a-z]{1,})\s+[a-z]{1,}\s+[0-9]{2,}-[a-z]{1,}-[0-9]{4,}$/i) { $shape = trim($1); }
}
close(GBFF) or die "error close file $!:";
open(SUM, ">>", $summary) or die "error open file $!:";
print SUM $pubmedId . "\t" . $nucleScore . "\t" . $classification ."\t" ;
print SUM $country . "\t" . $host . "\t" . $isoSource . "\t" . $aPercent . "\t" ;
print SUM $tPercent . "\t" . $gPercent . "\t" . $cPercent ."\t" . $nPercent . "\t";
print SUM $GCpercent ."\t". $atgcRatio ."\t". $length . "\t". $shape."\n";
close(SUM) or die "error close file: $!";
if (%componentsSumHash) {
write_assembly_component($fnaFile, $genomeName, \%componentsSumHash, $log);
}
}
#------------------------------------------------------------------------------
# get assembly component
sub write_assembly_component {
my($fnaFile, $genomeName, $componentsSumHashRef, $log) = @_;
my %componentsSumHash = %{$componentsSumHashRef};
my $status = "na";
my $level = "na";
my $gcpercent;
my $tmp_fasta_file = "sequence.txt";
my @desc = ();
# check each sequence from (multi-)fasta file
my ($seq, $inputfile);
if ($log) {$log->msg(1, "search specific components");}
# extract sequence details
my $seqIO = Bio::SeqIO->new(-format=>'Fasta', -file=>$fnaFile);
while ($seq = $seqIO->next_seq()) {
my $seqID = $seq->id; # ID of sequence
my $seqDesc = $seq->desc; # Description of sequence
my $globalSeq = $seq->seq;
my $seqLength = $seq->length();
open(TSEQ, ">", $tmp_fasta_file) or die "Error open file: $!";
print TSEQ $globalSeq;
close(TSEQ);
my ($ade, $thy, $gua, $cyt, $n, $length) = number_nuc_length_seq($tmp_fasta_file);
my ($aPercent, $tPercent, $gPercent, $cPercent, $nPercent) = nucleotid_percent($ade, $thy, $gua, $cyt, $n, $length);
$gcpercent = gc_percent($globalSeq);
@desc = split /,/, $seqDesc;
if ($desc[1]) { $level = $desc[1]; }
foreach my $component (keys %componentsSumHash) {
if ($desc[0] =~ /$component/) {
$status = $component;
my $info = $seqID . "\t" . $genomeName ."\t" . $seqDesc . "\t" . $seqLength . "\t" . $status . "\t" . $level ."\t";
$info.= $gcpercent."\t". $aPercent ."\t". $tPercent ."\t". $gPercent ."\t". $cPercent . "\n";
add_to_file($componentsSumHash{$component}, $info);
if ($log) {$log->msg(1, "found component $component");}
}
}
}
}
#------------------------------------------------------------------------------
# download fasta sequence and report on ENA with assembly ID
sub get_fasta_and_report_sequence_ena_assembly {
my($sequenceID) = @_;
my $tmp_file = "fichier.txt";
my @id_list = ();
my $id_chain = "";
my $fasta_file = "";
my $report_file = "";
my $url = "https://www.ebi.ac.uk/ena/data/view/$sequenceID&display=xml";
my $output = get($url);
open(TMP, ">", $tmp_file) or die("could not open $!");
print TMP $output;
close(TMP) or die("could not close $!");
open(TMP, "<", $tmp_file) or die("could not open $!");
while(<TMP>){
if($_ =~ /<CHROMOSOME accession="(.*)">/){
push(@id_list, $1)
}
}
close(TMP) or die("could not close $!");
$id_chain = join(",", @id_list);
$url = "https://www.ebi.ac.uk/ena/data/view/$id_chain&display=fasta";
$output = get($url);
$fasta_file = $sequenceID . ".fasta";
open(FILE, ">", $fasta_file) or die("could not open $!");
print FILE $output;
close(FILE) or die("could not close $!");
$report_file = $sequenceID . "_report.txt";
for my $id (@id_list) {
$url = "https://www.ebi.ac.uk/ena/data/view/$id&display=text&header=true";
$output = get($url);
open(FILE, ">>", $report_file) or die("could not open $!");
print FILE $output;
print FILE "##########################################################################\n\n";
close(FILE) or die("could not close $!");
}
unlink "fichier.txt" or die "error delete file :$!";
return ($fasta_file, $report_file);
}
#------------------------------------------------------------------------------
# download ENA
sub sequence_ena {
my($sequenceID, $log) = @_;
my $assemblyRep = $sequenceID . "_folder";
my $fastaFile;
my $reportFile;
if(-d $assemblyRep) { rmtree($assemblyRep); }
mkdir $assemblyRep;
if ($log) {$log->msg(1, "ENA sequence download\n");}
if ($log) {$log->msg(1, "Creation of repository: $assemblyRep\n");}
if($sequenceID =~ /^GCA_.*/){
($fastaFile, $reportFile) = get_fasta_and_report_sequence_ena_assembly($sequenceID);
}
else {
($fastaFile, $reportFile) = get_fasta_and_report_sequence_ena_other($sequenceID);
}
if ($log) {$log->msg(1, "Download of ENA fasta and report files for sequence: $sequenceID\n");}
move($fastaFile, $assemblyRep) or die "move failed: $!";
move($reportFile, $assemblyRep) or die "move failed: $!";
if ($log) {$log->msg(1, "Move fasta and report files to folder\n");}
}
#------------------------------------------------------------------------------
# download fasta sequence and report on ENA with ENA ID
sub get_fasta_and_report_sequence_ena_other {
my($sequenceID) = @_;
my $fasta_file = "";
my $report_file = "";
my $url;
my $output;
$url = "https://www.ebi.ac.uk/ena/data/view/$sequenceID&display=fasta";
$output = get($url);
$fasta_file = $sequenceID . ".fasta";
open(FILE, ">", $fasta_file) or die("could not open $!");
print FILE $output;
close(FILE) or die "could not close $!";
$url = "https://www.ebi.ac.uk/ena/data/view/$sequenceID&display=text&header=true";
$output = get($url);
$report_file = $sequenceID . "_report.txt";
open(FILE, ">>", $report_file) or die "could not open: $!";
print FILE $output;
close(FILE) or die "could not close $!";
return ($fasta_file, $report_file);
}
#------------------------------------------------------------------------------
# add information to file
sub add_to_file {
my ($file, $info) = @_;
open(FILE, ">>", $file) or die ("Could not open $!");
print FILE $info;
close(FILE);
}
#------------------------------------------------------------------------------
# return taxonomic rank of species by tax id
sub get_taxonomic_rank {
my($tax_id, $taxonomic_file) = @_;
my $species = "na";
my $genus = "na";
my $family = "na";
my $order = "na";
my $class = "na";
my $phylum = "na";
# my ($species,$genus,$family,$order,$class,$phylum);
my @tmp_array = ($species, $genus, $family, $order, $class, $phylum);
open(TFILE, "<", $taxonomic_file) or
die("Could not open $taxonomic_file: $!");
while(<TFILE>) {
chomp;
my @tax_info = split(/\|/, $_);
if ($tax_info[0] == $tax_id) {
@tax_info = trim_array(@tax_info);
$tmp_array[0] = $tax_info[1];
splice(@tax_info, 0, 3);
for(my $i = 1; $i < $#tmp_array + 1; $i++) {
if (length($tax_info[$i-1]) > 0) { $tmp_array[$i] = $tax_info[$i-1]; }
}
close(TFILE) or die "error close $taxonomic_file $!:";
return @tmp_array;
}
}
close(TFILE) or die "error close $taxonomic_file $!:";
}
#------------------------------------------------------------------------------
# write html summary file
sub write_html_summary {
my($summary) = @_;
my $htmlFile = "summary.html";
my $header = "";
my @fileToRead = ();
open(HTML, ">", $htmlFile) or die "error open HTML summary $!";
print HTML "<!DOCTYPE html>\n";
print HTML "<html>\n";
print HTML " <head>\n";
print HTML " <title>Assembly summary</title>\n";
print HTML " </head>\n";
print HTML " <body>\n";
print HTML " <h2>Assembly Summary</h2>\n";
close(HTML) or die "error close HTML summary $!";
open(SUM, "<", $summary) or die "error open tsv summary $!";
@fileToRead = <SUM>;
close(SUM) or die "error close tsv summary $!";
$header = splice(@fileToRead, 0, 1);
for my $line (@fileToRead) {
write_html_table($line, $htmlFile, $header);
}
open(HTML, ">>", $htmlFile) or die "error open HTML summary $!";
print HTML " </body>\n";
print HTML "</html>\n";
close(HTML) or die "error close HTML summary $!";
}
#------------------------------------------------------------------------------
# write html table for summary
sub write_html_table {
my ($line, $htmlFile, $header) = @_;
open(HTML, ">>", $htmlFile) or die "error open HTML summary $!";
print HTML " <table border=\"1\" style=\"margin-bottom: 20px;\">\n";
close(HTML) or die "error close HTML summary $!";
add_table_content($line, $htmlFile, $header);
}
#------------------------------------------------------------------------------
# add information to table
sub add_table_content {
my ($line, $htmlFile, $headers) = @_;
my @assemblyHeader = split(/\t/, $headers);
my @assemblyInfo = split(/\t/, $line);
my %hashHeaderInfo;
my $nbOfCell = 7;
my $fullLine = floor(($#assemblyHeader + 1) / $nbOfCell);
my $restCell = $#assemblyHeader + 1 - $fullLine * $nbOfCell;
for (my $i = 0; $i < $#assemblyHeader + 1; $i++) {