sci-biology/full_lengther_next: version bump

Package-Manager: portage-2.2.26

3 files changed, 266 insertions, 1 deletions

diff --git a/sci-biology/full_lengther_next/Manifest b/sci-biology/full_lengther_next/Manifest
index 6b1755016..04acafb04 100644
--- a/sci-biology/full_lengther_next/Manifest
+++ b/sci-biology/full_lengther_next/Manifest
@@ -1 +1 @@
-DIST full_lengther_next-0.0.8.gem 38912 SHA256 2808de8e04aea2118176ad04298a33e49e60048c8ef7d0f332d98308ae2d4664 SHA512 73c299f564c1580d737be49426e1363b171fcccea81b849f7311da328b6011b99847f28685266f6faebcb128d5f63c787dc27028f009ed25641e1b66ae6cfcf6 WHIRLPOOL 672ce60224cc431f2565b40ca583f9377ffc1c93b55e8a6b7f8055e467be7753edcdfd35f716316d37cc29c4c56759dc8c4a26a1b25ffcfaadd361218cc3422a
+DIST full_lengther_next-0.5.6.gem 2038784 SHA256 3e2afada6feada3e4503679a113d9b898061beb27e989c2fe40d35b331f9a417 SHA512 af81e72e3f2e21a0cd013ded12df69d7b877986eb4392691931d93c25acce87c5dec04346b5efa37ccb43a0f3aceabaca7f4cf2a99d5ae679325b18329548b7b WHIRLPOOL 2313280bf69fe2c1b34f81125fa3a1882bf410b106bf53c35e0fe410dea5b38f97cf23bdb7e1bdaa8eb0c52dfe5a53c335904e021431068b8ee99043e457ac8d
diff --git a/sci-biology/full_lengther_next/files/download_fln_dbs.rb b/sci-biology/full_lengther_next/files/download_fln_dbs.rb
new file mode 100644
index 000000000..90eacbbb8
--- /dev/null
+++ b/sci-biology/full_lengther_next/files/download_fln_dbs.rb
@@ -0,0 +1,260 @@
+#!/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 = $2
+		else
+			my_fasta += line
+		end
+	end
+	
+	return isoform_hash
+end
+
+################################################### MAIN
+
+ROOT_PATH=File.dirname(__FILE__)
+
+if ENV['BLASTDB'] && File.exists?(ENV['BLASTDB'])
+  formatted_db_path = ENV['BLASTDB']
+else # otherwise use ROOTPATH + DB
+  formatted_db_path = File.expand_path(File.join(ROOT_PATH, "blast_dbs"))
+end
+
+ENV['BLASTDB']=formatted_db_path
+puts "Databases will be downloaded at: #{ENV['BLASTDB']}"
+puts "\nTo set the path for storing databases, execute next line in your terminal or add it to your .bash_profile:\n\n\texport BLASTDB=/my_path/\n\n"
+
+my_array = ["human","fungi","invertebrates","mammals","plants","rodents","vertebrates"]
+# my_array = ["plants","human"] # used for a shoter test
+
+conecta_uniprot(my_array, formatted_db_path)
+system('gunzip '+File.join(formatted_db_path,'*.gz'))
+
+isoform_hash = {}
+isoform_hash = load_isoform_hash(File.join(formatted_db_path, "uniprot_sprot_varsplic.fasta"))
+
+download_ncrna(formatted_db_path)
+
+my_array.each do |db_group|
+
+	filter_incomplete_seqs(File.join(formatted_db_path, "uniprot_sprot_#{db_group}.dat"), isoform_hash, formatted_db_path)
+	filter_incomplete_seqs(File.join(formatted_db_path, "uniprot_trembl_#{db_group}.dat"), isoform_hash, formatted_db_path)
+	
+	sp_fasta=File.join(formatted_db_path,"sp_#{db_group}","sp_#{db_group}.fasta")
+	tr_fasta=File.join(formatted_db_path,"tr_#{db_group}","tr_#{db_group}.fasta")
+	system("makeblastdb -in #{sp_fasta} -dbtype 'prot' -parse_seqids")
+	system("makeblastdb -in #{tr_fasta} -dbtype 'prot' -parse_seqids")
+	
+end
+
+puts "download_fln_dbs.rb has finished"
diff --git a/sci-biology/full_lengther_next/full_lengther_next-0.0.8.ebuild b/sci-biology/full_lengther_next/full_lengther_next-0.5.6.ebuild
index 0465bc02e..52412c00a 100644
--- a/sci-biology/full_lengther_next/full_lengther_next-0.0.8.ebuild
+++ b/sci-biology/full_lengther_next/full_lengther_next-0.5.6.ebuild
@@ -28,3 +28,8 @@ RDEPEND="${DEPEND}
 	>=sci-biology/scbi_mapreduce-0.0.29
 	>=sci-biology/scbi_plot-0.0.6
 	>=dev-ruby/xml-simple-1.0.12"
+
+#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
+#}