1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212
|
#!/usr/bin/env ruby
#
# vs-genes.rb - homology/motif search wrapper
#
# FASTA/BLAST/Pfam interface for the multiple query in the FASTA format
#
# Copyright (C) 2001 KATAYAMA Toshiaki <k@bioruby.org>
#
# 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 2 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.
#
# $Id: vs-genes.rb,v 0.1 2001/06/21 08:26:31 katayama Exp $
#
def usage(cpu, ktup, skip, resultdir, verbose)
print <<-END
Usage:
% #{$0} -p PROG -q QUERY -t TARGET [-c #] [-k #] [-s #] [-d DIR] [-v on]
options
-p PROG : (fasta3|ssearch3|tfasta3|fastx3|tfastx3)[3]
or
(blastp|blastn|blastx|tblastn|tblastx)
or
(hmmpfam|hmmpfam_n)
-q QUERY : query nucleotide or peptide sequences in the FASTA format
-t TARGET : target DB (FASTA or BLAST2 formatdb or Pfam format)
optional arguments
-c num : number of CPUs (for the SMP machines, default is #{cpu})
-k num : FASTA ktup value (2 for pep, 6 for nuc, default is #{ktup})
-s num : skip query (for the resume session, default is #{skip})
-d DIR : result output directory (default is "#{resultdir}")
-v on/off : verbose output of processing if on (default is "#{verbose}")
END
exit 1
end
### initialize
def init
arg = {}
# default values
arg['c'] = 1 # num of CPUs
arg['k'] = 2 # ktup value for FASTA
arg['s'] = 0 # skip query
arg['d'] = "./result" # result directory
arg['v'] = 'off' # verbose mode
# parse options
ARGV.join(' ').scan(/-(\w) (\S+)/).each do |key, val|
arg[key] = val
end
# check program, query, target or print usage
unless arg['p'] and arg['q'] and arg['t']
usage(arg['c'], arg['k'], arg['s'], arg['d'], arg['v'])
end
# create result output directory
unless test(?d, "#{arg['d']}")
Dir.mkdir("#{arg['d']}", 0755)
end
# print status
if arg['v'] != 'off'
puts "PROG : #{arg['p']}"
puts " ktup : #{arg['k']}" if arg['p'] =~ /fast/
puts "QUERY : #{arg['q']}"
puts " skip : #{arg['s']}"
puts "TARGET : #{arg['t']}"
puts "RESULT : #{arg['d']}"
end
return arg
end
### generate command line
def cmd_line(arg, orf)
# program with default command line options # query -> target DB
opt = {
# FASTA : "-b n" for best n scores, "-d n" for best n alignment
'fasta3' => "fasta3 -Q -H -m 6", # pep -> pep or nuc -> nuc
'ssearch3' => "ssearch3 -Q -H -m 6", # pep -> pep or nuc -> nuc
'tfasta3' => "tfasta3 -Q -H -m 6", # pep -> nuc
'fastx3' => "fastx3 -Q -H -m 6", # nuc -> pep
'tfastx3' => "tfastx3 -Q -H -m 6", # pep -> nuc (with frameshifts)
'fasta33' => "fasta33 -Q -H -m 6", # pep -> pep or nuc -> nuc
'ssearch33' => "ssearch33 -Q -H -m 6", # pep -> pep or nuc -> nuc
'tfasta33' => "tfasta33 -Q -H -m 6", # pep -> nuc
'fastx33' => "fastx33 -Q -H -m 6", # nuc -> pep
'tfastx33' => "tfastx33 -Q -H -m 6", # pep -> nuc (with frameshifts)
# BLAST : outputs XML
'blastp' => "blastall -m 7 -p blastp -d", # pep -> pep
'blastn' => "blastall -m 7 -p blastn -d", # nuc -> nuc
'blastx' => "blastall -m 7 -p blastx -d", # nuc -> pep
'tblastn' => "blastall -m 7 -p tblastn -d", # pep -> nuc
'tblastx' => "blastall -m 7 -p tblastx -d", # nuc -> nuc (by trans)
# Pfam : "-A n" for best n alignment, "-E n" for E value cutoff etc.
'hmmpfam' => "hmmpfam", # pep -> Pfam DB
'hmmpfam_n' => "hmmpfam -n", # nuc -> Pfam DB
}
# arguments used in the command line
cpu = arg['c'].to_i
ktup = arg['k']
target = arg['t']
query = arg['d'] + "/query." + orf
result = arg['d'] + "/" + orf
prog = opt[arg['p']]
if cpu > 1 # use multiple CPUs
case arg['p']
when /(fast|ssearch)/
prog += " -T #{cpu}"
prog.sub!(' ', '_t ') # rename program with "_t"
when /pfam/
prog += " --cpu #{cpu}"
end
end
# generate complete command line to execute
case arg['p']
when /fast/
command = "#{prog} #{query} #{target} #{ktup} > #{result}"
when /ssearch/
command = "#{prog} #{query} #{target} > #{result}"
when /blast/
command = "#{prog} #{target} -i #{query} > #{result}"
when /pfam/
command = "#{prog} #{target} #{query} > #{result}"
end
return command
end
### main
begin
arg = init
count = 0
open(arg['q'], "r") do |f|
while seq = f.gets("\n>")
count += 1
# skip (-s option)
next unless count > arg['s'].to_i
# clean up
seq.sub!(/^>?[ \t]*/, '') # delete '>' and SPACEs or TABs at the head
seq.sub!(/>$/, '') # delete '>' at the tail (separator)
# get ORF name
if seq[/^$/] # no definition (e.g. ">\nSEQ>" or ">\n>")
next # -> useless for the multiple query
else
orf = seq[/^\S+/] # the first word in the definition line
end
# KEGG uses ">DB:ENTRY" format in the definition line
if orf =~ /:/
db,orf = orf.split(/:/)
end
# add time if the same ORF name was already used
if test(?f, "#{arg['d']}/#{orf}")
orf = "#{orf}.#{Time.now.to_f.to_s}"
end
# create temporal file of the query
open("#{arg['d']}/query.#{orf}", "w+") do |tmp|
tmp.print(">#{seq}")
end
command = cmd_line(arg, orf)
# print status
if arg['v'] != 'off'
puts "#{count} : #{orf} ..."
puts " #{command}"
end
# execute
system("#{command}")
# remove temporal file
File.delete("#{arg['d']}/query.#{orf}")
end
end
end
|