mapp2g 0.1.5 → 0.2.0

checksums.yaml

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

@@ -26,6 +26,9 @@ Usage: mapp2g [options]
     -h, --help                       show this help message and exit
 ```
 
+Query sequences should be in FASTA format. Multiple sequences can be included in one file.
+
+
 (example)
 ```
 mapp2g -q human_genome.fasta -q p53.protein.fasta
@@ -37,6 +40,18 @@ Reference genomes should be formated in blastdb before running mapp2g. blastdb c
 makeblastdb -in human_genome.fasta -dbtype nucl -parse_seqids
 ```
 
+## Outputs
+
+For each query, the following files are generated.
+
+- query sequence in fasta
+- blast output in tab-delmited format (format 6)
+- exonerate full output
+- exonerate alignment in gff3 format
+- report.json
+
+report.json contains all of the information above in json line format.
+
 
 ## License
 

data/exe/mapp2g

@@ -1,9 +1,11 @@
 #!/usr/bin/env ruby
 
-require "mapp2g"
+#require_relative '../lib/mapp2g' # for development
+require 'mapp2g'
 require 'bio'
 require 'tempfile'
 require 'optparse'
+require 'json'
 
 ### Parse options
 
@@ -75,6 +77,8 @@ end
 
 ### Main
 
+report_json_lines = []
+
 Dir.mkdir(outdir)
 
 Bio::FlatFile.open(Bio::FastaFormat, query).each_with_index do |fas, i|
@@ -83,14 +87,42 @@ Bio::FlatFile.open(Bio::FastaFormat, query).each_with_index do |fas, i|
   tf.close
   id = (i + 1).to_s
   query_file_path = "#{outdir}/#{id}.fasta"
-  out_file_path = "#{outdir}/#{id}.exonerate.txt"
   File.open(query_file_path, "w"){|o| o.puts fas}
 
   mapper = Mapp2g::Mapper.new()
   res = mapper.run(query_file_path, genome)
-  File.open(out_file_path, "w"){|o| o.puts res}
+  if res
+    out_file_path = "#{outdir}/#{id}.exonerate.txt"
+    File.open(out_file_path, "w"){|o| o.puts res[:exonerate_result]}
+    out_file_path = "#{outdir}/#{id}.blast.txt"
+    File.open(out_file_path, "w"){|o| o.puts res[:blast_result]}
+    gff3 = Mapp2g::ExonerateOutput.new(res[:exonerate_result]).to_gff3()
+    out_file_path = "#{outdir}/#{id}.exonerate.gff3"
+    File.open(out_file_path, "w"){|o| o.puts gff3}
+
+    report = {
+      "runtime_id" => id,
+      "query_id" => fas.entry_id, 
+      "query_fasta" => fas.to_s,
+      "exonerate" => res[:exonerate_result], 
+      "blast" => res[:blast_result], 
+      "gff3" => gff3
+    }
+    report_json_lines << report.to_json
+
+  else
+    report = {
+      "runtime_id" => id,
+      "query_id" => fas.entry_id,
+      "query_fasta" => fas.to_s,
+      "exonerate" => nil,
+      "blast" => nil,
+      "gff3" => nil
+    }
+    STDERR.puts "No hit for #{fas.entry_id}"
+  end
 
-  gff3 = Mapp2g::ExonerateOutput.new(res).to_gff3()
-  out_file_path = "#{outdir}/#{id}.exonerate.gff3"
-  File.open(out_file_path, "w"){|o| o.puts gff3}
 end
+
+report_json = report_json_lines.join("\n")
+File.open("#{outdir}/report.json", "w"){|o| o.puts report_json}

data/lib/mapp2g/mapper.rb

@@ -4,9 +4,9 @@ module Mapp2g
 
   class Mapper
 
-    EVALUE_DEFAULT = 1.0e-8
+    EVALUE_DEFAULT = 1.0e-5
     NCPU_DEFAULT = 4
-    MAX_HSP_INTERVAL = 50000
+    MAX_HSP_INTERVAL = 400000
     EXTENSION = 50000
     TMPDIR_DEFAULT = Dir.tmpdir
 
@@ -15,11 +15,11 @@ module Mapp2g
 
     ## step 1: tblastn
     def exec_tblastn_to_know_rough_target_region(query, genome, evalue=EVALUE_DEFAULT, ncpu=NCPU_DEFAULT)
-      cmd = "tblastn -db #{genome} -query #{query} -max_target_seqs 40 -soft_masking yes -seg yes -outfmt 6 -evalue #{evalue} -num_threads #{ncpu} "
+      cmd = "tblastn -db #{genome} -query #{query} -max_target_seqs 40 -soft_masking yes -seg yes -outfmt 6 -evalue #{evalue} -num_threads #{ncpu} -culling_limit 2"
       # puts cmd
       res = nil
-      IO.popen(cmd){|io| res = io.read}
-      # puts res
+      IO.popen(cmd){|io| res = io.read} 
+#     STDERR.puts res
       if res == ""
       ## no hit
         return nil
@@ -27,7 +27,7 @@ module Mapp2g
         lines = []
         prev_chr = nil
         res.split(/\n/).each do |l|
-      #    p prev_chr
+#          p prev_chr
           a = l.chomp.split(/\t/)
           unless prev_chr
             lines << l
@@ -42,7 +42,7 @@ module Mapp2g
         a = lines.shift.chomp.split(/\t/)
         left, right = [a[8].to_i, a[9].to_i].sort
         
-        STDERR.puts [left, right].inspect
+#        STDERR.puts [left, right].inspect
     
         lines.each do |l|
           a = l.chomp.split(/\t/)
@@ -57,14 +57,16 @@ module Mapp2g
             break
           end
         end
-      #  p [left, right]
+#        STDERR.puts [left, right].inspect
         
         top_chromosome = res.split(/\n/)[0].split(/\t/)[1]
         h = {
           :top_chromosome => top_chromosome, 
           :left => left,
-          :right => right
+          :right => right,
+          :blast_result => res
         }
+#        STDERR.puts h.inspect
         return h
       end
     end
@@ -117,8 +119,10 @@ module Mapp2g
         tf.close
       
         exonerate_result = exec_exonerate(query, tf.path)
-        return exonerate_result
-      
+        return {
+          :blast_result => hit[:blast_result], 
+          :exonerate_result => exonerate_result
+        }
       else
         return nil
       end

data/lib/mapp2g/version.rb

@@ -1,5 +1,5 @@
 # frozen_string_literal: true
 
 module Mapp2g
-  VERSION = "0.1.5"
+  VERSION = "0.2.0"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: mapp2g
 version: !ruby/object:Gem::Version
-  version: 0.1.5
+  version: 0.2.0
 platform: ruby
 authors:
 - Shuji Shigenobu
 autorequire: 
 bindir: exe
 cert_chain: []
-date: 2023-07-15 00:00:00.000000000 Z
+date: 2023-07-17 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