commit: 85fe7624385b5d424a1d250106a55c4aad74217f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Apr 26 12:07:50 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Apr 26 12:07:50 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=85fe7624
sci-biology/full_lengther_next: version bump
Package-Manager: portage-2.2.28
.../full_lengther_next/files/download_fln_dbs.rb | 260 ---------------------
....5.7.ebuild => full_lengther_next-0.6.0.ebuild} | 7 +-
2 files changed, 1 insertion(+), 266 deletions(-)
diff --git a/sci-biology/full_lengther_next/files/download_fln_dbs.rb
b/sci-biology/full_lengther_next/files/download_fln_dbs.rb
deleted file mode 100644
index 90eacbb..0000000
--- a/sci-biology/full_lengther_next/files/download_fln_dbs.rb
+++ /dev/null
@@ -1,260 +0,0 @@
-#!/usr/bin/env ruby
-
-# 15-2-2011 Noe Fernandez-Pozo
-# Script to download Full-LengtherNext databases.
-# Once in UniProtKB/Swiss-Prot, a protein entry is removed from
UniProtKB/TrEMBL.
-
-require 'net/ftp'
-require 'open-uri'
-
-class FtpClient
-
-def initialize
-end
-
-def connect(server)
- @server=server
-end
-
-def login
-
-end
-
-def chdir(dir)
- @dir=dir
-end
-
-def getbinaryfile(file,output_file)
- if !File.exists?(output_file) &&
!File.exists?(output_file.gsub('.gz',''))
- puts " - Downloading"
- cmd="wget #{@server}/#{@dir}/#{file} -O #{output_file}"
- system(cmd)
- else
- puts "File #{output_file}, or #{output_file.gsub('.gz','')} already
exists. Skip download"
- end
-
-end
-
-def close
-end
-
-end
-################################################### Functions
-
-def download_ncrna(formatted_db_path)
-
- if !File.exists?(File.join(formatted_db_path, "nc_rna_db"))
- Dir.mkdir(File.join(formatted_db_path, "nc_rna_db"))
- end
-
- puts "Downloading ncRNA database"
- open(File.join(formatted_db_path, "nc_rna_db/ncrna_fln_100.fasta.zip"),
"wb") do |my_file|
- my_file.print
open('http://www.scbi.uma.es/downloads/FLNDB/ncrna_fln_100.fasta.zip').read
- end
- puts "\nncRNA database downloaded"
-
-
ncrna_zip=File.join(formatted_db_path,'nc_rna_db','ncrna_fln_100.fasta.zip')
- ncrna_out_dir=File.join(formatted_db_path,'nc_rna_db')
- system("unzip", ncrna_zip, "-d", ncrna_out_dir)
- system("rm", ncrna_zip)
-
- puts "\nncRNA database decompressed"
-
-
ncrna_fasta=File.join(formatted_db_path,'nc_rna_db','ncrna_fln_100.fasta')
- system("makeblastdb", "-in", ncrna_fasta, "-dbtype", "nucl",
"-parse_seqids")
-
- puts "\nncRNA database completed"
-end
-
-def conecta_uniprot(my_array, formatted_db_path)
-
- #$ftp = Net::FTP.new()
- $ftp = FtpClient.new()
-
- if !File.exists?(formatted_db_path)
- Dir.mkdir(formatted_db_path)
- end
-
- $ftp.connect('ftp://ftp.uniprot.org')
-
- $ftp.login
-
- puts "connected to UniProt"
-
- my_array.each do |db_group|
- puts "Downloading #{db_group}"
- download_uniprot(db_group, formatted_db_path)
- end
-
-
varsplic_out=File.join(formatted_db_path,'uniprot_sprot_varsplic.fasta.gz')
-
$ftp.chdir("/pub/databases/uniprot/current_release/knowledgebase/complete")
- $ftp.getbinaryfile("uniprot_sprot_varsplic.fasta.gz", varsplic_out)
-
- puts "isoform files downloaded"
-
- $ftp.close
-
-end
-
-def download_uniprot(uniprot_group, formatted_db_path)
-
-
sp_out=File.join(formatted_db_path,"uniprot_sprot_#{uniprot_group}.dat.gz")
-
tr_out=File.join(formatted_db_path,"uniprot_trembl_#{uniprot_group}.dat.gz")
-
$ftp.chdir("/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions")
- puts " from
ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_sprot_#{uniprot_group}.dat.gz"
- puts " from
ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/taxonomic_divisions/uniprot_trembl_#{uniprot_group}.dat.gz"
- $ftp.getbinaryfile("uniprot_sprot_#{uniprot_group}.dat.gz", sp_out)
- $ftp.getbinaryfile("uniprot_trembl_#{uniprot_group}.dat.gz", tr_out)
-
- puts "#{uniprot_group} files downloaded"
-
-end
-
-def filter_incomplete_seqs(file_name, isoform_hash, formatted_db_path)
-
- puts "filtering sequences from #{file_name}"
-
- # UniProtKB fragments with FT NON_CONS and FT NON_TER features.
- #
- # * FT NON_TER: The residue at an extremity of the sequence is not
the terminal residue. If applied to position 1, this signifies that the first
position is not the N-terminus of the complete molecule. If applied to the last
position, it means that this position is not the C-terminus of the complete
molecule. There is no description field for this key. Examples of NON_TER key
feature lines:
- # FT NON_TER 1 1
- # FT NON_TER 29 29
- # * FT NON_CONS: Non-consecutive residues. Indicates that two
residues in a sequence are not consecutive and that there are a number of
unreported or missing residues between them. Example of a NON_CONS key feature
line:
- # FT NON_CONS 1683 1684
- #
- # NON_CONS fragments are not indicated as non-consecutive in InterPro
and being non-consecutive the match to methods may be incorrect if the method
spans the 'break'.
-
- newseq=false
- print_seq=true
- id=''
- description = ''
- organism_name = ''
- seq = ''
- organelle = ''
-
- file_name =~ /uniprot_([a-z]+)_([a-z]+).dat/
- db_name = $1
- output_name = $2
- db_name.sub!('sprot','sp')
- db_name.sub!('trembl','tr')
-
- if !File.exists?(File.join(formatted_db_path,
"#{db_name}_#{output_name}"))
- Dir.mkdir(File.join(formatted_db_path,
"#{db_name}_#{output_name}"))
- end
-
- output_file = File.new(File.join(formatted_db_path,
"#{db_name}_#{output_name}/#{db_name}_#{output_name}.fasta"), "w")
-
- File.open(file_name).each_line do |line|
- if (newseq == false)
- if (line =~ /^AC\s+(\w+);/)
- id=$1
- newseq = true
- description = ''
- organism_name = ''
- seq = ''
- print_seq = true
- organelle = ''
- end
- else
- if (line =~ /^DE\s+(.+)\;*/)
- if (description == '')
- description = $1
- description.sub!(/RecName: Full=/,'sp=')
- description.sub!(/SubName: Full=/,'tr=')
- end
- if (line =~ /Flags: Fragment/)
- # puts "#{id} #{line}"
- print_seq=false
- end
- elsif (line =~ /^OS\s+(.+)/)
- organism_name = $1
- elsif (line =~ /^OG\s+(.+)/)
- organelle = $1
- elsif (line =~ /^FT\s+NON_TER\s+/)
- print_seq=false
- # puts "#{id} NON_TER"
- elsif (line =~ /^FT\s+NON_CONS\s+(\d+)\s+/)
- print_seq=false
- # puts "#{id} NON_CONS"
- elsif (line =~ /^\s+([\w\s]+)/)
- seq += $1
- elsif (line =~ /^\/\//)
- seq.gsub!(/\s*/,'')
- if (seq !~ /^M/i)
- print_seq=false
- end
- newseq = false
-
- if (print_seq)
- output_file.puts ">#{id} #{description}
#{organism_name} #{organelle}\n#{seq}"
- if (!isoform_hash[id].nil?)
- output_file.puts
isoform_hash[id]
- end
- end
- end
- end
- end
- output_file.close
-end
-
-def load_isoform_hash(file)
-
- isoform_hash = {}
- my_fasta = ''
- acc = ''
- File.open(file).each do |line|
- line.chomp!
- if (line =~ /(^>\w+\|(\w+)\-\d\|.+)/)
- if (isoform_hash[acc].nil?)
- isoform_hash[acc]= "#{my_fasta}\n"
- else
- isoform_hash[acc]+= "#{my_fasta}\n"
- end
- my_fasta = "#{$1}\n"
- acc = $2
- else
- my_fasta += line
- end
- end
-
- return isoform_hash
-end
-
-################################################### MAIN
-
-ROOT_PATH=File.dirname(__FILE__)
-
-if ENV['BLASTDB'] && File.exists?(ENV['BLASTDB'])
- formatted_db_path = ENV['BLASTDB']
-else # otherwise use ROOTPATH + DB
- formatted_db_path = File.expand_path(File.join(ROOT_PATH, "blast_dbs"))
-end
-
-ENV['BLASTDB']=formatted_db_path
-puts "Databases will be downloaded at: #{ENV['BLASTDB']}"
-puts "\nTo set the path for storing databases, execute next line in your
terminal or add it to your .bash_profile:\n\n\texport BLASTDB=/my_path/\n\n"
-
-my_array =
["human","fungi","invertebrates","mammals","plants","rodents","vertebrates"]
-# my_array = ["plants","human"] # used for a shoter test
-
-conecta_uniprot(my_array, formatted_db_path)
-system('gunzip '+File.join(formatted_db_path,'*.gz'))
-
-isoform_hash = {}
-isoform_hash = load_isoform_hash(File.join(formatted_db_path,
"uniprot_sprot_varsplic.fasta"))
-
-download_ncrna(formatted_db_path)
-
-my_array.each do |db_group|
-
- filter_incomplete_seqs(File.join(formatted_db_path,
"uniprot_sprot_#{db_group}.dat"), isoform_hash, formatted_db_path)
- filter_incomplete_seqs(File.join(formatted_db_path,
"uniprot_trembl_#{db_group}.dat"), isoform_hash, formatted_db_path)
-
-
sp_fasta=File.join(formatted_db_path,"sp_#{db_group}","sp_#{db_group}.fasta")
-
tr_fasta=File.join(formatted_db_path,"tr_#{db_group}","tr_#{db_group}.fasta")
- system("makeblastdb -in #{sp_fasta} -dbtype 'prot' -parse_seqids")
- system("makeblastdb -in #{tr_fasta} -dbtype 'prot' -parse_seqids")
-
-end
-
-puts "download_fln_dbs.rb has finished"
diff --git a/sci-biology/full_lengther_next/full_lengther_next-0.5.7.ebuild
b/sci-biology/full_lengther_next/full_lengther_next-0.6.0.ebuild
similarity index 82%
rename from sci-biology/full_lengther_next/full_lengther_next-0.5.7.ebuild
rename to sci-biology/full_lengther_next/full_lengther_next-0.6.0.ebuild
index 1f3476f..64d300a 100644
--- a/sci-biology/full_lengther_next/full_lengther_next-0.5.7.ebuild
+++ b/sci-biology/full_lengther_next/full_lengther_next-0.6.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -32,8 +32,3 @@ RDEPEND="${DEPEND}
>=sci-biology/scbi_plot-0.0.6
>=dev-ruby/xml-simple-1.0.12
>=dev-ruby/gnuplot-2.3.0"
-
-#src_prepare(){
-# cp "${FILESDIR}"/download_fln_dbs.rb all/full_lengther_next-0.0.8/bin
|| die
-# chmod a+rx all/full_lengther_next-0.0.8/bin/*.rb || die
-#}
