aai 0.5.0 → 0.5.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 26efeea51af3369c265b1bda2c7ea1540884ebfb
-  data.tar.gz: fed2bdcddcfe2fb67540515494aae9ec260a1c59
+  metadata.gz: c439cf060023c9dc0c792217b3983f08bf3f696e
+  data.tar.gz: 6f091a4758dcde5648cf4f611b74fe6a21c163b0
 SHA512:
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-  data.tar.gz: f39b404ae3a7a5c494a99a1fc505b9894375c63878fe9d40bcb09e7701b610d80c6501297ea7fc9d42e1fdc5bf5809d4fb28dfb8b888152415a7d30ab9a29003
+  metadata.gz: d54827285835cab1981111b4c3b17de121385ba85f9c999158621e73eec063660c8d27161e83f34c055135f835c905cc4d7fc5f96aa4263f003e5fdde1e4219a
+  data.tar.gz: c34a2a154b613e7cfeab1cb009508803e933dfcf085fde8dea6ade437e731f4f296644672d6b1516f9ebc7e8335da8a0f39f5f5d19f3806e1b837c35c7718dce

data/exe/aai

@@ -12,6 +12,7 @@ include AbortIf::Assert
 
 Aai.extend Aai
 Aai.extend Aai::Utils
+Time.extend Aai::CoreExtensions::Time
 
 def move_files fnames, dest
   fnames.each do |fname|
@@ -41,7 +42,7 @@ opts = Trollop.options do
 end
 
 abort_if opts[:infiles].nil? || opts[:infiles].empty?,
-         "No infiles given"
+         "No infiles given. Try #{__FILE__} --help for help."
 
 Aai.check_command "blastp"
 Aai.check_command "makeblastdb"
@@ -49,34 +50,66 @@ Aai.check_command "parallel"
 
 Aai.check_files opts[:infiles]
 
+abort_if File.exists?(opts[:outdir]),
+         "#{opts[:outdir]} already exists. Choose a new outdir."
+
 FileUtils.mkdir_p opts[:outdir]
 
-seq_lengths, clean_fnames = Aai.process_input_seqs! opts[:infiles]
+seq_lengths = nil
+clean_fnames = nil
+blast_db_basenames = nil
+btabs = nil
+best_hits = nil
+one_way = nil
+two_way = nil
+aai_strings = nil
+score_dir = nil
+outf = nil
+
+Time.time_it "Processing input seqs", AbortIf.logger do
+  seq_lengths, clean_fnames = Aai.process_input_seqs! opts[:infiles]
+end
 
-blast_db_basenames = Aai.make_blastdbs! clean_fnames,
-                                        opts[:cpus]
+Time.time_it "Making blast databases", AbortIf.logger do
+  blast_db_basenames = Aai.make_blastdbs! clean_fnames,
+                                          opts[:cpus]
+end
 
-btabs = Aai.blast_permutations! clean_fnames,
-                                blast_db_basenames,
-                                opts[:cpus]
+Time.time_it "Running blast jobs", AbortIf.logger do
+  btabs = Aai.blast_permutations! clean_fnames,
+                                  blast_db_basenames,
+                                  opts[:cpus]
+end
 
-best_hits = Aai.get_best_hits btabs, seq_lengths
+Time.time_it "Getting best hits", AbortIf.logger do
+  best_hits = Aai.get_best_hits btabs, seq_lengths
+end
 
-one_way = Aai.one_way_aai best_hits
+Time.time_it "Getting one way hits", AbortIf.logger do
+  one_way = Aai.one_way_aai best_hits
+end
 
-two_way = Aai.two_way_aai best_hits
+Time.time_it "Getting two way hits", AbortIf.logger do
+  two_way = Aai.two_way_aai best_hits
+end
 
-aai_strings = Aai.aai_strings one_way, two_way
+Time.time_it "Making aai strings", AbortIf.logger do
+  aai_strings = Aai.aai_strings one_way, two_way
+end
 
-score_dir = File.join opts[:outdir], "aai_scores"
-FileUtils.mkdir_p score_dir
-outf = File.join score_dir, "#{opts[:basename]}.aai.txt"
-File.open(outf, "w") do |f|
-  Aai.aai_strings(one_way, two_way).each do |str|
-    f.puts str
+Time.time_it "Writing score file", AbortIf.logger do
+  score_dir = File.join opts[:outdir], "aai_scores"
+  FileUtils.mkdir_p score_dir
+  outf = File.join score_dir, "#{opts[:basename]}.aai.txt"
+  File.open(outf, "w") do |f|
+    Aai.aai_strings(one_way, two_way).each do |str|
+      f.puts str
+    end
   end
 end
 
+AbortIf.logger.info { "Cleaning up" }
+
 blast_db_dir = File.join opts[:outdir], "blastdbs"
 btab_dir = File.join opts[:outdir], "btabs"
 clean_fasta_dir = File.join opts[:outdir], "clean_fastas"

data/lib/aai.rb

@@ -63,48 +63,10 @@ module Aai
               "--query #{query} --db #{db} --out #{out} " +
               "--evalue #{EVALUE_CUTOFF}"
 
-        Process.run_it! cmd
-
-        # if exit_status.zero?
-        #   completed_outf_names << out
-        # else
-        #   failed_jobs << idx
-        #   AbortIf.logger.warn { "Blast job failed. Non-zero exit status " +
-        #                         "(#{exit_status}) " +
-        #                         "when running '#{cmd}'. " +
-        #                         "Will retry at end." }
-        # end
-
-        # [completed_outf_names, failed_jobs]
+        Process.run_and_time_it! "Diamond blast", cmd
       end
     end
 
-    # if failed_jobs.count > 0
-    #   Time.time_it "Retrying failed blast jobs" do
-    #     # retry failed jobs once
-    #     Parallel.each(failed_jobs, in_processes: cpus) do |idx|
-    #       query = args[idx][0]
-    #       db    = args[idx][1]
-    #       out   = args[idx][2]
-
-    #       cmd = "diamond blastp --threads #{cpus} --outfmt 6 " +
-    #             "--query #{query} --db #{db} --out #{out} " +
-    #             "--evalue #{EVALUE_CUTOFF}"
-
-    #       exit_status = Process.run_it cmd
-
-    #       if exit_status.zero?
-    #         completed_outf_names << out
-    #       else
-    #         AbortIf.logger.error { "Retrying blast job failed. " +
-    #                                "Non-zero exit status " +
-    #                                "(#{exit_status}) " +
-    #                                "when running '#{cmd}'." }
-    #       end
-    #     end
-    #   end
-    # end
-
     outf_names
   end
 
@@ -123,7 +85,7 @@ module Aai
         cmd = "diamond makedb --threads 1 --in #{fname} " +
               "--db #{fname}#{BLAST_DB_SUFFIX}"
 
-        Process.run_it! cmd
+        Process.run_and_time_it! "Make db", cmd
       end
     end
 
@@ -256,34 +218,43 @@ module Aai
     genome_pair_keys = one_way_hits.keys.map { |pair| pair.sort }.uniq
 
     genome_pair_keys.each do |pair_key|
-      AbortIf.abort_unless one_way_hits.has_key?(pair_key) &&
-                           one_way_hits.has_key?(pair_key.reverse),
-                           "Missing keys for #{pair_key}"
+      if one_way_hits.has_key?(pair_key) &&
+         one_way_hits.has_key?(pair_key.reverse)
 
-      forward_hits = one_way_hits[pair_key]
-      reverse_hits = one_way_hits[pair_key.reverse]
+        forward_hits = one_way_hits[pair_key]
+        reverse_hits = one_way_hits[pair_key.reverse]
 
-      combinations = one_way_combinations forward_hits, reverse_hits
+        combinations = one_way_combinations forward_hits, reverse_hits
 
-      two_way_hits = combinations.select do |h1, h2|
-        two_way_hit? h1, h2
-      end
+        two_way_hits = combinations.select do |h1, h2|
+          two_way_hit? h1, h2
+        end
 
-      two_way_hit_info = two_way_hits.map do |h1, h2|
-        { genome_pair: [h1[:query_genome],
-                        h1[:target_genome]].sort,
-          pident: (h1[:pident] + h2[:pident]) / 2.0 }
-      end
+        two_way_hit_info = two_way_hits.map do |h1, h2|
+          { genome_pair: [h1[:query_genome],
+                          h1[:target_genome]].sort,
+            pident: (h1[:pident] + h2[:pident]) / 2.0 }
+        end
 
-      two_way_hit_info.each do |hit|
-        if two_way_aai.has_key? hit[:genome_pair]
-          two_way_aai[hit[:genome_pair]] << hit[:pident]
-        else
-          two_way_aai[hit[:genome_pair]] = [hit[:pident]]
+        two_way_hit_info.each do |hit|
+          if two_way_aai.has_key? hit[:genome_pair]
+            two_way_aai[hit[:genome_pair]] << hit[:pident]
+          else
+            two_way_aai[hit[:genome_pair]] = [hit[:pident]]
+          end
         end
+      elsif !one_way_hits.has_key?(pair_key)
+        AbortIf.logger.warn { "No pair info for #{pair_key}. " +
+                              "No two way hits possible " +
+                              "for #{pair_key}." }
+      elsif !one_way_hits.has_key?(pair_key.reverse)
+        AbortIf.logger.warn { "No pair info for #{pair_key.reverse}. " +
+                              "No two way hits possible " +
+                              "for #{pair_key}." }
       end
     end
 
+    # outside of genome_pair_keys.each
     two_way_aai.map do |genome_pair, pidents|
       [genome_pair, pidents.reduce(:+) / pidents.length.to_f]
     end.to_h

data/lib/aai/core_extensions.rb

@@ -44,7 +44,7 @@ module Aai
         exit_status = self.run_it *a, &b
 
         AbortIf.abort_unless exit_status.zero?,
-                             "ERROR: non-zero exit status " +
+                             "Non-zero exit status " +
                              "(#{exit_status}) " +
                              "when running '#{a.inspect}', " +
                              "'#{b.inspect}'"

data/lib/aai/version.rb

@@ -1,5 +1,5 @@
 module Aai
-  VERSION = "0.5.0"
+  VERSION = "0.5.1"
   COPYRIGHT = "2017 Ryan Moore"
   CONTACT   = "moorer@udel.edu"
   WEBSITE   = "https://github.com/mooreryan/aai"

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: aai
 version: !ruby/object:Gem::Version
-  version: 0.5.0
+  version: 0.5.1
 platform: ruby
 authors:
 - Ryan Moore