mapp2g 0.1.2 → 0.1.4

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -1,34 +1,42 @@
 # Mapp2g
 
-TODO: Delete this and the text below, and describe your gem
-
-Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/mapp2g`. To experiment with that code, run `bin/console` for an interactive prompt.
-
 ## Installation
 
-TODO: Replace `UPDATE_WITH_YOUR_GEM_NAME_PRIOR_TO_RELEASE_TO_RUBYGEMS_ORG` with your gem name right after releasing it to RubyGems.org. Please do not do it earlier due to security reasons. Alternatively, replace this section with instructions to install your gem from git if you don't plan to release to RubyGems.org.
+### Pre-requisites
 
-Install the gem and add to the application's Gemfile by executing:
+  * NCBI blast
+  * exonerate
+  
+These two software should be installed. mapp2g is wrtten in Ruby. Ruby sholud be installed.
 
-    $ bundle add UPDATE_WITH_YOUR_GEM_NAME_PRIOR_TO_RELEASE_TO_RUBYGEMS_ORG
+### Install mapp2g using gem
 
-If bundler is not being used to manage dependencies, install the gem by executing:
-
-    $ gem install UPDATE_WITH_YOUR_GEM_NAME_PRIOR_TO_RELEASE_TO_RUBYGEMS_ORG
+```
+gem install mapp2g
+```
 
 ## Usage
 
-TODO: Write usage instructions here
-
-## Development
+```
+Usage: mapp2g [options]
+    -q, --query QUERY                query amino acid sequences in FASTA format
+    -g, --genome BLASTDB             genome reference as blastdb
+    -o, --outdir [OUTDIR]            output directory. DEFAULT: mapp2g_out_{process_id}
+    -v, --version                    show version number
+    -h, --help                       show this help message and exit
+```
 
-After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+(example)
+```
+mapp2g -q human_genome.fasta -q p53.protein.fasta
+```
 
-To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and the created tag, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+Reference genomes should be formated in blastdb before running mapp2g. blastdb can be made as follws:
 
-## Contributing
+```
+makeblastdb -in human_genome.fasta -dbtype nucl -parse_seqids
+```
 
-Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/mapp2g.
 
 ## License
 

data/exe/mapp2g

@@ -5,6 +5,7 @@ require 'bio'
 require 'tempfile'
 require 'optparse'
 
+### Parse options
 
 opt = OptionParser.new
 OPTS = {}
@@ -15,14 +16,21 @@ begin
     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("-q QUERY", "--query", "query amino acid sequences in FASTA format. REQUIRED."){|v| OPTS[:q] = v}
+  opt.on("-g BLASTDB", "--genome", "genome reference as blastdb. REQUIRED."){|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
+
+  if ARGV.size == 0
+    puts opt
+    exit
+  end
+
   opt.parse!(ARGV)
+
 rescue => e
   puts "ERROR: #{e}\nSee #{opt}"
   exit
@@ -36,6 +44,34 @@ outdir = (OPTS[:o] || "mapp2g_out_#{$$}")
 
 #p [query, genome, outdir]
 
+### Check environment
+
+def command?(name)
+  `which #{name}`
+  unless $?.success?
+    raise "#{name} command not found"
+  end
+end
+
+begin
+  command?("exonerate")
+  command?("blastn")
+rescue => e
+  puts "ERROR: #{e}"
+  exit(1)
+end
+
+begin
+  unless File.exist?("#{genome}.nsq") && File.exist?("#{genome}.nos")
+    raise "genome is not indexed. Please run 'makeblastdb -in #{genome} -dbtype nucl -parse_seqids'"
+  end
+rescue => e
+  puts "ERROR: #{e}"
+  exit(1)
+end
+
+### Main
+
 Dir.mkdir(outdir)
 
 Bio::FlatFile.open(Bio::FastaFormat, query).each_with_index do |fas, i|

data/lib/mapp2g/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Mapp2g
-  VERSION = "0.1.2"
+  VERSION = "0.1.4"
 end

data/scripts/add_annotation_from_uniprot_fasta_to_gff.rb

@@ -0,0 +1,117 @@
+#===
+# add_annotation_from_uniprot_fasta_to_gff.rb
+#
+# This script adds annotation from UniProt FASTA file to GFF file.
+# 
+# Usage: ruby add_annotation_from_uniprot_fasta_to_gff.rb <uniprot_proteome_referene_fasta> <gff> 
+# 
+# Example: ruby add_annotation_from_uniprot_fasta_to_gff.rb UP000001593_45351.fasta mygff.gff3 > mygff_with_annotation.gff3
+# 
+
+require 'uri'
+
+# https://www.uniprot.org/help/fasta-headers
+#
+# UniProtKB
+#
+# >db|UniqueIdentifier|EntryName ProteinName OS=OrganismName OX=OrganismIdentifier [GN=GeneName ]PE=ProteinExistence SV=SequenceVersion
+#
+# Where:
+#
+#     db is 'sp' for UniProtKB/Swiss-Prot and 'tr' for UniProtKB/TrEMBL.
+#     UniqueIdentifier is the primary accession number of the UniProtKB entry.
+#     EntryName is the entry name of the UniProtKB entry.
+#     ProteinName is the recommended name of the UniProtKB entry as annotated in the RecName field. For UniProtKB/TrEMBL entries without a RecName field, the SubName field is used. In case of multiple SubNames, the first one is used. The 'precursor' attribute is excluded, 'Fragment' is included with the name if applicable.
+#     OrganismName is the scientific name of the organism of the UniProtKB entry.
+#     OrganismIdentifier is the unique identifier of the source organism, assigned by the NCBI.
+#     GeneName is the first gene name of the UniProtKB entry. If there is no gene name, OrderedLocusName or ORFname, the GN field is not listed.
+#     ProteinExistence is the numerical value describing the evidence for the existence of the protein.
+#     SequenceVersion is the version number of the sequence.
+
+# >db|UniqueIdentifier|EntryName ProteinName OS=OrganismName OX=OrganismIdentifier [GN=GeneName ]PE=ProteinExistence SV=SequenceVersion
+
+fastaf = ARGV[0]
+gfff = ARGV[1]
+data = Hash.new
+
+
+module Escape
+
+  # ref: https://github.com/bioruby/bioruby/blob/master/lib/bio/db/gff.rb
+
+  # unsafe characters to be escaped for normal columns
+  UNSAFE = /[^-_.!~*'()a-zA-Z\d\/?:@+$\[\] "\x80-\xfd><;=,]/n
+
+  # unsafe characters to be escaped for seqid columns
+  # and target_id of the "Target" attribute
+  UNSAFE_SEQID = /[^-a-zA-Z0-9.:^*$@!+_?|]/n
+
+  # unsafe characters to be escaped for attribute columns
+  UNSAFE_ATTRIBUTE = /[^-_.!~*'()a-zA-Z\d\/?:@+$\[\] "\x80-\xfd><]/n
+
+  URI_PARSER = URI::Parser.new
+
+  def self.escape_attribute(str)
+    URI_PARSER.escape(str, UNSAFE_ATTRIBUTE)
+  end
+
+end
+
+File.open(fastaf).each do |l|
+  if /^>/.match(l)
+#    puts l
+    m = /^>(\S+)\|(\S+)\|(\S+)\s+(.+)\s+OS\=(.+)\s+OX\=(\d+)\s+(GN\=(.+)\s+)?PE\=(\d+)\s+SV\=(\d+)/.match(l)
+    db = m[1]
+    id = m[2]
+    entry_name = m[3]
+    protein_name = m[4]
+    organism_name = m[5]
+    organism_id = m[6]
+    gene_name = m[8]
+    prot_exis = m[9]
+    seq_ver = m[10]
+
+    h = {
+      :db => db,
+      :id => id,
+      :entry_name => entry_name,
+      :protein_name => protein_name,
+      :organism_name => organism_name,
+      :organism_id => organism_id,
+      :gene_name => gene_name,
+      :prot_exis => prot_exis,
+      :seq_ver => seq_ver
+    }
+    data[id] = h
+
+#    p [db, id, entry_name, protein_name, organism_name, organism_id]
+  end
+
+end
+
+File.open(gfff).each do |l|
+  a = l.chomp.split(/\t/)
+  col_type = a[2]
+  col_attr = a[8]
+  if col_type == "match"
+    id = /ID\=(.+)/.match(col_attr)[1]
+#    p id
+    d = data[id]
+    h = Hash.new
+    dbxref = Hash.new
+    h['Name'] = Escape.escape_attribute(d[:protein_name])
+    dbxref['EMBL'] = d[:id]
+    dbxref['Uniprot'] = d[:entry_name]
+    dbxref['tax'] = d[:organism_id]
+    h['Dbxref'] = dbxref.map{|k, v| "#{k}:#{Escape.escape_attribute(v)}"}.join(",")
+    if d[:gene_name]
+      h['Alias'] = [Escape.escape_attribute(d[:gene_name])].join(",")
+    end
+    new_attr_col = col_attr + ";" + h.map{|k, v| "#{k}=#{v}"}.join(";")
+    b = a.dup
+    b[8] = new_attr_col
+    puts b.join("\t")
+  else
+    puts l
+  end
+end

data/scripts/mapp2g-exonerate_gff2_to_jbgff3.v2.rb

@@ -0,0 +1,37 @@
+gff_lines = []
+
+i = 0
+name = nil
+target = nil
+
+ARGF.each do |l|
+  
+  if m = /\s+Query:\s/.match(l)
+    name = m.post_match.chomp.split[0]
+    i+=1
+    STDERR.puts "#{i} records processed" if i % 1000 == 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
+    gff_lines <<  b.join("\t")
+  end
+
+end
+
+puts gff_lines
+

data/scripts/mapp2g-exonerate_gff2_to_jbgff3.v3.rb

@@ -0,0 +1,70 @@
+#!/bin/env ruby
+
+exonerate_out = (ARGV[0] || "mapp2g_out_ClyHem/mapp2g_out_ClyHem_j609t87/57.exonerate.txt")
+
+query_name = nil
+target = nil
+cigar = nil
+gff2_lines = []
+#vulgar = nil
+
+File.open(exonerate_out, "r").each do |l|
+
+  if m = /\s+Query:\s/.match(l)
+    query_name = m.post_match.chomp.split[0]
+  elsif m = /\s+Target:\s/.match(l)
+    target = m.post_match.split[0]
+  elsif m = /^cigar:\s/.match(l)
+    cigar = m.post_match.chomp
+  elsif /^#{target}/.match(l) &&
+      (/\texonerate:est2genome\t/.match(l) || /\texonerate:protein2genome:local\t/.match(l)) &&
+      (/\texon\t/.match(l) || /\tgene\t/.match(l))
+    gff2_lines << l.chomp
+  end
+
+end
+
+#puts gff2_lines
+
+gff2_lines.each do |l|
+  a = l.chomp.split(/\t/)
+  b = Array.new(9)
+  a.each_with_index{|x, i| b[i] = x}
+  if b[2] == "gene"
+    b[2] = "match"
+    orig_attribute = b[8].split(";").map{|x| x.strip.split(/\s+/)}.to_h
+#    p orig_attribute
+    c = cigar.split(/\s+/)
+    cigar_pairs = c[9..-1].join.scan(/[MDI]\d+/)
+    attribute = {'ID' => query_name,
+                 'Target' => [query_name, c[1].to_i + 1, c[2]].join(" "),
+                 'Gap'=> cigar_pairs.join(" "),
+                 'identity' => orig_attribute['identity'],
+                 'similarity' => orig_attribute['similarity']}
+    b[8] = attribute.map{|k, v| "#{k}=#{v}"}.join(";")
+  elsif b[2] == "exon"
+    b[2] = "match_part"
+    orig_attribute = b[8].split(";").map{|x| x.strip.split(/\s+/)}.to_h
+    attribute = {'Parent' => query_name,
+    'identity' => orig_attribute['identity'],
+    'similarity' => orig_attribute['similarity']}
+    b[8] = attribute.map{|k, v| "#{k}=#{v}"}.join(";")
+
+  else
+    raise
+  end
+  puts b.join("\t")
+end
+
+
+# CIGAR format
+# The format starts with the same 9 fields as sugar output (see above), and is followed by a series of <operation, length> pairs where operation is one of match, insert or delete, and the length describes the number of times this operation is repeated.
+# 1 query_id: Query identifier
+# 2 query_start: Query position at alignment start
+# 3 query_end: Query position alignment end
+# 4 query_strand: Strand of query matched
+# 5 target_id|
+# 6 target_start| the same 4 fields
+# 7 target_end  | for the target sequence
+# 8 target_strand|
+# 9 score| The raw alignment score

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: mapp2g
 version: !ruby/object:Gem::Version
-  version: 0.1.2
+  version: 0.1.4
 platform: ruby
 authors:
 - Shuji Shigenobu
-autorequire:
+autorequire: 
 bindir: exe
 cert_chain: []
-date: 2023-02-05 00:00:00.000000000 Z
+date: 2023-07-09 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
@@ -30,7 +30,10 @@ files:
 - lib/mapp2g/mapper.rb
 - lib/mapp2g/version.rb
 - mapp2g.gemspec
+- scripts/add_annotation_from_uniprot_fasta_to_gff.rb
 - scripts/mapp2g-exonerate_gff2_to_jbgff3.rb
+- scripts/mapp2g-exonerate_gff2_to_jbgff3.v2.rb
+- scripts/mapp2g-exonerate_gff2_to_jbgff3.v3.rb
 - sig/mapp2g.rbs
 homepage: https://github.com/shujishigenobu/mapp2g
 licenses:
@@ -39,7 +42,7 @@ metadata:
   homepage_uri: https://github.com/shujishigenobu/mapp2g
   source_code_uri: https://github.com/shujishigenobu/mapp2g
   changelog_uri: https://github.com/shujishigenobu/mapp2g
-post_install_message:
+post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
@@ -54,8 +57,8 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.2.15
-signing_key:
+rubygems_version: 3.4.10
+signing_key: 
 specification_version: 4
 summary: mapp2g is the tool to map protein sequences to genome references in a splicing-aware
   way.