-
Notifications
You must be signed in to change notification settings - Fork 20
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
334bd2f
commit 5d27851
Showing
124 changed files
with
4,229 additions
and
0 deletions.
There are no files selected for viewing
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Large diffs are not rendered by default.
Oops, something went wrong.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,4 @@ | ||
>spQ7F1X5 rice | ||
MADRAPPPPPPPAGIDSRSGFCAATRIFHSTRAPGDLPPESLPMTAAAYAFSLLSSSTLPGRPALVDAATGIAISYPSFLAAVRSLAGGLWCSLGLRPGDVALVVAPSRLEVPVLDFALMSIGAVVSPANPVSTPEEYAHQVALSRPVVAFAAPEVAAKLPEHVRCVVIGSDEYGRLAASDGRRAAAPAAVAVKQSDTAAVLYSSGTTGRVKAVAITHRNLIALMSLHADNREKVAREAAEAGEEPPPPAVTLLPIPLFHVFGFMMVLRSVSMGETSVLMERFDFIAALRAIERYRVTLLPAAPPVLVAMVKYEEARRRDLSSLLVIGIGGAPLGREVAEQFASVFPNVELVQGYGLTESSGAVAATVGPEESKAYGSVGKLGSHLQAKIVDPSTGYVGDDEATAATVDSEGWLKTGDLCYFNEDGFLYIVDRLKELIKYKGYQVPPAELEHILQSHPGIADAAVIPYPDEEAGELPMAFIVRQPGSNITKEQVMDYVAKQVAPYKKVRRVAFVTAIPKSPAGKILRRELVQQALSMGASKL | ||
>SequenceA FromApisMellifera | ||
MLPQTPDIIPTTLNQQKCVKARALYDNIAEAPDELAFRKGDVLTVLEQNTAGLEGWWLCALRGRQGICPGNRLRLLVGQYDTGGCLVGSRPDLTISEDGIQRHGKRRSWHVQPNRVVTPQKCGDVYLYDLPASRGSPAPPSRHDSPLNSNNEHLHNSGRYTTSSRNSVDNGGDVSDCYDVPPRAIPVIPSPASSPSPAPSCYDIPRPPTSCTPISNCSGGSGVTPLDCYDVPRPLQPLTPSSSASSLTNDGSLSGSNRSSLAAPDYDVPRSRLPASSLPSRHNTPVPKTPTPPPPPQTQQIYDVPVSKELPLELDSALEGLQRLQSEASAAIARLLGFVSPVWRTPQRLDATLMDLRLAALRLRTSLHDLAEFAEGTLGNAGKAPDKGLATKLRPLVKALRDSDKLVQEAATELDAMEWDAGKLCRGGGDTPTPTNGPPSTILPPAQPDPLDQLIACARALTEDVRQVASFIQGNSTLLFKRSSIISTGSSNNSGAGEDYDYVNLDSREVVAKQREEVRASLPQELRSNYDLLVSESDNATIQMPPTTPTPMDPNDKQLLAFYAAQVITHGNHLTHAIDAFMQTVEHNQPPKVFLAHGKFVVLSAHRLVHIGDTVHRNVIRNDVKTRVLECANALNEALKQTVSKTKQAAQFFPSVSAVQEMVDSVVDVSHLAKDLKVAIINGAQQPMEVTSSNFQEVLVELDEILKNATFLCIDGEFTGLNSGPDGGVFDTPAQYYAKLRTGSMDFLLIQFGLSVFTFNKEMQKYNQRSYNFYVFPRPLNRMAPDCRFMCQTSSISFLASQGFDFNKLFKLGIPYLTTNEEEKLMKRLEEKQRIRDEGTEILPISDVERPQIEEICSRIDEFVTSETEELLIEKCNAFIRRLVYQEVKLRWPNKLKVESKMNNFGCILVVQRLGTKEEEEQREIEKREREKTEIQQAVGLSILMRKIADSGKLIVGHNMLLDLCHIVHQFFGQLPESYFEFKSLVHSLFPRILDTKIICHSQQFKENIPSSNLGILLETVSKSPFKITEVEPIDGRSYSTLSEKCHEAGYDAYITGICFIALSNYLGSLQKPEVPIVLSDSPLLNPFLNKLLIARLKDVPYINLVGDDPNPSRDHVFHLTFPKEWKFNDISHLFSPFGSVHVSWLSDISAYIELHRRDQVNEVMKVLAKTSTYKLQRYADYQASLENFNTGERKRKLSSSEETTPEAEELCGCRECAKIETETLCRA |
Binary file not shown.
Binary file not shown.
Binary file not shown.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,19 @@ | ||
# get Swissprot/trembl | ||
|
||
mkdir uniprot | ||
cd uniprot | ||
wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz | ||
##wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz | ||
|
||
gunzip uniprot_sprot.fasta.gz | ||
makeblastdb -dbtype prot -parse_seqids -title "UniProtKB-SwissProt" -in uniprot_sprot.fasta | ||
##makeblastdb -dbtype prot -parse_seqids -title "UniProtKB-TrEMBL" -in uniprot_trembl.fasta | ||
##cd .. | ||
|
||
|
||
### get NR | ||
##mkdir nr | ||
##cd nr | ||
##./update_blastdb.pl nr | ||
|
||
|
19 changes: 19 additions & 0 deletions
19
2023/data/reference_databases/download_reference_databases
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,19 @@ | ||
# get Swissprot/trembl | ||
|
||
mkdir uniprot | ||
cd uniprot | ||
wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz | ||
##wget ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz | ||
|
||
gunzip uniprot_sprot.fasta.gz | ||
makeblastdb -dbtype prot -parse_seqids -title "UniProtKB-SwissProt" -in uniprot_sprot.fasta | ||
##makeblastdb -dbtype prot -parse_seqids -title "UniProtKB-TrEMBL" -in uniprot_trembl.fasta | ||
##cd .. | ||
|
||
|
||
### get NR | ||
##mkdir nr | ||
##cd nr | ||
##./update_blastdb.pl nr | ||
|
||
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,271 @@ | ||
#! /usr/bin/perl -w | ||
# $Id: update_blastdb.pl,v 1.6 2005/09/09 18:58:39 camacho Exp $ | ||
# =========================================================================== | ||
# | ||
# PUBLIC DOMAIN NOTICE | ||
# National Center for Biotechnology Information | ||
# | ||
# This software/database is a "United States Government Work" under the | ||
# terms of the United States Copyright Act. It was written as part of | ||
# the author's official duties as a United States Government employee and | ||
# thus cannot be copyrighted. This software/database is freely available | ||
# to the public for use. The National Library of Medicine and the U.S. | ||
# Government have not placed any restriction on its use or reproduction. | ||
# | ||
# Although all reasonable efforts have been taken to ensure the accuracy | ||
# and reliability of the software and data, the NLM and the U.S. | ||
# Government do not and cannot warrant the performance or results that | ||
# may be obtained by using this software or data. The NLM and the U.S. | ||
# Government disclaim all warranties, express or implied, including | ||
# warranties of performance, merchantability or fitness for any particular | ||
# purpose. | ||
# | ||
# Please cite the author in any work or product based on this material. | ||
# | ||
# =========================================================================== | ||
# | ||
# Author: Christiam Camacho | ||
# | ||
# File Description: | ||
# Script to download the pre-formatted BLAST databases from the NCBI ftp | ||
# server. | ||
# | ||
# =========================================================================== | ||
|
||
use strict; | ||
use warnings; | ||
use Net::FTP; | ||
use Getopt::Long; | ||
use Pod::Usage; | ||
use File::stat; | ||
|
||
use constant VERSION => 1.2; | ||
use constant NCBI_FTP => "ftp.ncbi.nlm.nih.gov"; | ||
use constant BLAST_DB_DIR => "/blast/db"; | ||
use constant USER => "anonymous"; | ||
use constant PASSWORD => "anonymous"; | ||
use constant DEBUG => 0; | ||
|
||
# Process command line options | ||
my $opt_verbose = 1; | ||
my $opt_quiet = 0; | ||
my $opt_force_download = 0; | ||
my $opt_help = 0; | ||
my $opt_passive = 0; | ||
my $opt_timeout = 120; | ||
my $opt_showall = 0; | ||
my $result = GetOptions("verbose+" => \$opt_verbose, | ||
"quiet" => \$opt_quiet, | ||
"force" => \$opt_force_download, | ||
"passive" => \$opt_passive, | ||
"timeout=i" => \$opt_timeout, | ||
"showall" => \$opt_showall, | ||
"help" => \$opt_help); | ||
$opt_verbose = 0 if $opt_quiet; | ||
die "Failed to parse command line options\n" unless $result; | ||
pod2usage({-exitval => 0, -verbose => 2}) if $opt_help; | ||
pod2usage({-exitval => 1, -verbose => 2}) unless (scalar @ARGV or $opt_showall); | ||
|
||
|
||
# Connect and download files | ||
my $ftp = &connect_to_ftp(); | ||
if ($opt_showall) { | ||
print "$_\n" foreach (sort(&get_available_databases())); | ||
} else { | ||
my @files = sort(&get_files_to_download()); | ||
&download(@files); | ||
} | ||
$ftp->quit(); | ||
|
||
# Connects to NCBI ftp server | ||
sub connect_to_ftp | ||
{ | ||
my %ftp_opts; | ||
$ftp_opts{'Passive'} = 1 if $opt_passive; | ||
$ftp_opts{'Timeout'} = $opt_timeout if ($opt_timeout >= 0); | ||
$ftp_opts{'Debug'} = 1 if ($opt_verbose > 1); | ||
my $ftp = Net::FTP->new(NCBI_FTP, %ftp_opts) | ||
or die "Failed to connect to " . NCBI_FTP . ": $!\n"; | ||
$ftp->login(USER, PASSWORD) | ||
or die "Failed to login to " . NCBI_FTP . ": $!\n"; | ||
$ftp->cwd(BLAST_DB_DIR); | ||
$ftp->binary(); | ||
print STDERR "Connected to NCBI\n" if $opt_verbose; | ||
return $ftp; | ||
} | ||
|
||
# Gets the list of available databases on NCBI FTP site | ||
sub get_available_databases | ||
{ | ||
my @blast_db_files = $ftp->ls(); | ||
my @retval = (); | ||
|
||
foreach (@blast_db_files) { | ||
next unless (/\.tar\.gz$/); | ||
push @retval, &extract_db_name($_); | ||
} | ||
|
||
# Sort and eliminate adjacent duplicates | ||
@retval = sort @retval; | ||
my $prev = "not equal to $retval[0]"; | ||
return grep($_ ne $prev && ($prev = $_, 1), @retval); | ||
} | ||
|
||
# Obtains the list of files to download | ||
sub get_files_to_download | ||
{ | ||
my @blast_db_files = $ftp->ls(); | ||
my @retval = (); | ||
|
||
if (DEBUG) { | ||
print STDERR "DEBUG: Found the following files on ftp site:\n"; | ||
print STDERR "DEBUG: $_\n" for (@blast_db_files); | ||
} | ||
|
||
for my $requested_db (@ARGV) { | ||
for my $file (@blast_db_files) { | ||
next unless ($file =~ /\.tar\.gz$/); | ||
if ($file =~ /^$requested_db\..*/) { | ||
push @retval, $file; | ||
} | ||
} | ||
} | ||
|
||
if ($opt_verbose) { | ||
for my $requested_db (@ARGV) { | ||
unless (grep(/$requested_db/, @retval)) { | ||
print STDERR "$requested_db not found, skipping.\n" | ||
} | ||
} | ||
} | ||
|
||
return @retval; | ||
} | ||
|
||
# Download the requestes files only if they are missing or if they are newer in | ||
# the FTP site. | ||
sub download($) | ||
{ | ||
my @requested_dbs = @ARGV; | ||
|
||
for my $file (@_) { | ||
|
||
if ($opt_verbose and &is_multivolume_db($file)) { | ||
my $db_name = &extract_db_name($file); | ||
my $nvol = &get_num_volumes($db_name, @_); | ||
print STDERR "Downloading $db_name (" . $nvol . " volumes) ...\n"; | ||
} | ||
|
||
if ($opt_force_download or | ||
not -f $file or | ||
((stat($file))->mtime < $ftp->mdtm($file))) { | ||
print STDERR "Downloading $file... " if $opt_verbose; | ||
$ftp->get($file); | ||
print STDERR "done.\n" if $opt_verbose; | ||
} else { | ||
print STDERR "$file is up to date.\n" if $opt_verbose; | ||
} | ||
} | ||
} | ||
|
||
# Determine if a given pre-formatted BLAST database file is part of a | ||
# multi-volume database | ||
sub is_multivolume_db | ||
{ | ||
my $file = shift; | ||
return 1 if ($file =~ /\.\d{2}\.tar\.gz$/); | ||
return 0; | ||
} | ||
|
||
# Extracts the database name from the pre-formatted BLAST database archive file | ||
# name | ||
sub extract_db_name | ||
{ | ||
my $file = shift; | ||
my $retval = ""; | ||
if (&is_multivolume_db($file)) { | ||
$retval = $1 if ($file =~ m/(.*)\.\d{2}\.tar\.gz$/); | ||
} else { | ||
$retval = $1 if ($file =~ m/(.*)\.tar\.gz$/); | ||
} | ||
return $retval; | ||
} | ||
|
||
# Returns the number of volumes for a BLAST database given the file name of a | ||
# pre-formatted BLAST database and the list of all databases to download | ||
sub get_num_volumes | ||
{ | ||
my $db = shift; | ||
my $retval = 0; | ||
foreach (@_) { | ||
if (/$db/) { | ||
if (/.*\.(\d{2})\.tar\.gz$/) { | ||
$retval = int($1) if (int($1) > $retval); | ||
} | ||
} | ||
} | ||
return $retval + 1; | ||
} | ||
|
||
__END__ | ||
=head1 NAME | ||
B<update_blastdb.pl> - Download pre-formatted BLAST databases from NCBI | ||
=head1 SYNOPSIS | ||
update_blastdb.pl [options] blastdb ... | ||
=head1 OPTIONS | ||
=over 2 | ||
=item B<--showall> | ||
Show all available pre-formatted BLAST databases (default: false). The output | ||
of this option lists the database names which should be used when | ||
requesting downloads or updates using this script. | ||
=item B<--passive> | ||
Use passive FTP, useful when behind a firewall (default: false). | ||
=item B<--timeout> | ||
Timeout on connection to NCBI (default: 120 seconds). | ||
=item B<--force> | ||
Force download even if there is a archive already on local directory (default: | ||
false). | ||
=item B<--verbose> | ||
Increment verbosity level (default: 1). Repeat this option multiple times to | ||
increase the verbosity level (maximum 2). | ||
=item B<--quiet> | ||
Produce no output (default: false). Overrides the B<--verbose> option. | ||
=back | ||
=head1 DESCRIPTION | ||
This script will download the pre-formatted BLAST databases requested in the | ||
command line from the NCBI ftp site. | ||
=head1 EXIT CODES | ||
This script returns 0 on success and a non-zero value on errors. | ||
=head1 BUGS | ||
Please report them to <[email protected]> | ||
=head1 COPYRIGHT | ||
See PUBLIC DOMAIN NOTICE included at the top of this script. | ||
=cut |
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,7 @@ | ||
--- | ||
layout: page | ||
--- | ||
|
||
<!-- import the information that is provided in ssh.md --> | ||
|
||
{% include_relative ssh.md %} |
Oops, something went wrong.