#!/usr/bin/env ruby

# 15-2-2011 Noe Fernandez-Pozo
# Script to create your own Full-LengtherNext User database.

require 'net/ftp'

#receive one argument or fail
if (ARGV.size != 2)
	
	puts "incorrect number of arguments, you need a taxonomic group like 'Coniferopsida', you can search it in 'http://www.ncbi.nlm.nih.gov/Taxonomy/'
and a UniProt taxonomic group from this list:

	fungi
	human
	invertebrates
	mammals
	plants
	rodents
	vertebrates

mode of use: ruby make_user_db.rb coniferopsida plants\n\n"

  Process.exit(-1);
end

(my_group,uniprot_group)=ARGV

################################################### Functions

def filter_incomplete_seqs(output_file,file_name, my_group)
	
	puts " filtering sequences"
	
	# 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=false
	incomplete=false
	id=''
	description = ''
	organism_name = ''
	seq = ''
	organelle = ''
	
	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 = false
				incomplete = false
				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}"
					incomplete = true
				end
			elsif (line =~ /^OS\s+(.+)/)
				organism_name = $1
			elsif (line =~ /^OG\s+(.+)/)
				organelle = $1
			elsif (line =~ /^OC\s+[\w\s\;]*#{my_group}/i) && (!incomplete)
				print_seq=true
				# puts "#{id}   #{organism_name} print_seq?: #{print_seq}"
			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}"
				end
			end
		end
	end
end

########################################################
##  MAIN
########################################################

ROOT_PATH=File.dirname(__FILE__)

# $: << File.expand_path(File.join(ROOT_PATH, "classes"))

# load gem path, only to test locally
# $: << File.expand_path('~/progs/ruby/gems/full_lengther_next/lib')

require 'full_lengther_next'

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


if !File.exists?(File.join(ENV['BLASTDB'], my_group))
	Dir.mkdir("blast_dbs/#{my_group}")
end

output_file_path=File.join(ENV['BLASTDB'],my_group,my_group+".fasta")

output_file = File.new(output_file_path, "w")

filter_incomplete_seqs(output_file, File.join(ENV['BLASTDB'], "uniprot_sprot_#{uniprot_group}.dat"), my_group)
filter_incomplete_seqs(output_file, File.join(ENV['BLASTDB'], "uniprot_trembl_#{uniprot_group}.dat"), my_group)

output_file.close

`makeblastdb -in #{output_file_path} -dbtype 'prot' -parse_seqids`

puts "make_user_db.rb has finished"