mapp2g 0.1.1 → 0.1.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
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-  data.tar.gz: f1bba896fb88a7f7c9ce5b59cd35169403f4bcfed08def326173c914d9841667
+  metadata.gz: 2d3b7c217addd7e92a9b0dc4d2af710c216d7dbcf86c2416018ac80bee287e1c
+  data.tar.gz: 562dbf402617e18af3b2e32cb32fb1e5f157ec783aaa6b61f2f44a5cf3877acc
 SHA512:
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+  metadata.gz: 6df38d0b72858bd49d354d0b72eeca57a70cfc80a075444bcffd8ecfcd4b59945395a76a3d38e70caea74254bce0e62f82039f15db6ca23566204444bc9bb5b2
+  data.tar.gz: 01174fd8de53e2e5f7d6a3021ff8789b242a53af4d8968bc3eaf6c3e1c67795826af82b95e7f0c1290e6c9d888d560d4488de5f1de4774c78d3b793dd52f2dcf

data/exe/mapp2g

@@ -3,11 +3,38 @@
 require "mapp2g"
 require 'bio'
 require 'tempfile'
+require 'optparse'
 
-query = ARGV[0]
-genome = ARGV[1]
-outdir = (ARGV[2] || "mapp2g_out_#{$$}")
-mapp2g_exe = "./mapp2g.rb"
+
+opt = OptionParser.new
+OPTS = {}
+
+begin
+  #opt.banner = "Usage: #{opt.program_name} [options] QUERY GENOME "
+  opt.on_tail("-v", "--version", "show version number") do
+    puts Mapp2g::VERSION
+    exit
+  end
+  opt.on("-q QUERY", "--query", "query amino acid sequences in FASTA format"){|v| OPTS[:q] = v}
+  opt.on("-g BLASTDB", "--genome", "genome reference as blastdb"){|v| OPTS[:g] = v}
+  opt.on("-o [OUTDIR]", "--outdir", "output directory. DEFAULT: mapp2g_out_{process_id}"){|v| OPTS[:o] = v}
+  opt.on_tail('-h', '--help', 'show this help message and exit') do
+    puts opt
+    exit
+  end
+  opt.parse!(ARGV)
+rescue => e
+  puts "ERROR: #{e}\nSee #{opt}"
+  exit
+end
+
+# p OPTS
+
+query = OPTS[:q]
+genome = OPTS[:g]
+outdir = (OPTS[:o] || "mapp2g_out_#{$$}")
+
+#p [query, genome, outdir]
 
 Dir.mkdir(outdir)
 

data/lib/mapp2g/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Mapp2g
-  VERSION = "0.1.1"
+  VERSION = "0.1.2"
 end

data/scripts/mapp2g-exonerate_gff2_to_jbgff3.rb

@@ -0,0 +1,28 @@
+name = nil
+target = nil
+ARGF.each do |l|
+  
+  if m = /\s+Query:\s/.match(l)
+    name = m.post_match.chomp.split[0]
+  elsif m = /\s+Target:\s/.match(l)
+    target = m.post_match.split[0]
+  elsif /^#{target}/.match(l) &&
+      (/\texonerate:est2genome\t/.match(l) || /\texonerate:protein2genome:local\t/.match(l)) &&
+      (/\tcds\t/.match(l) || /\texon\t/.match(l) || /\tgene\t/.match(l))
+#    puts l
+    a = l.chomp.split(/\t/)
+    b = Array.new(9)
+    a.each_with_index{|x, i| b[i] = x}
+    if b[2] == "gene"
+      b[-1] = "ID=#{name}"
+      b[2] = "match"
+    elsif (b[2] == "cds" || b[2] == "exon")
+      b[-1] = "Parent=#{name}"
+      b[2] = "match_part"
+    else
+      raise
+    end
+    puts b.join("\t")
+  end
+
+end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: mapp2g
 version: !ruby/object:Gem::Version
-  version: 0.1.1
+  version: 0.1.2
 platform: ruby
 authors:
 - Shuji Shigenobu
 autorequire:
 bindir: exe
 cert_chain: []
-date: 2023-02-04 00:00:00.000000000 Z
+date: 2023-02-05 00:00:00.000000000 Z
 dependencies: []
 description: mapp2g is a bioinformatics software, which map and align protein sequences
   (amino acid sequences) to genome references in a splicing-aware way. mapp2g alignment
@@ -30,6 +30,7 @@ files:
 - lib/mapp2g/mapper.rb
 - lib/mapp2g/version.rb
 - mapp2g.gemspec
+- scripts/mapp2g-exonerate_gff2_to_jbgff3.rb
 - sig/mapp2g.rbs
 homepage: https://github.com/shujishigenobu/mapp2g
 licenses: