bio-hmmer3_report 0.0.1 → 0.1.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 9279db9072373e76e70581cc5b0936a0cd229191
+  data.tar.gz: 2ea741942401e70f4fb1ba155a0f351c4d527d4c
+SHA512:
+  metadata.gz: 730dea0d04c44f88c23a75c47fa50c692d18310b1b71df36806616eebdfbb5608fc9fc38319d67118c0a91cee6abc61904c951eb630f9e40282e659690cae4f9
+  data.tar.gz: 7a3a4effa90354ba7a1caba1167d95349b514164d95d142f5cb10e3b98b842eade5ab1a6a035414c4ca05ab23254247b2de29c56685bbd6613564d2ef3214716

data/Gemfile

@@ -2,14 +2,16 @@ source "http://rubygems.org"
 # Add dependencies required to use your gem here.
 # Example:
 #   gem "activesupport", ">= 2.3.5"
+gem 'bio-logger', '~> 1.0'
 
 # Add dependencies to develop your gem here.
 # Include everything needed to run rake, tests, features, etc.
 group :development do
-  gem "shoulda", ">= 0"
-  gem "rdoc", "~> 3.12"
-  gem "jeweler", "~> 1.8.3"
-  gem "bundler", ">= 1.0.21"
-  gem "bio", ">= 1.4.2"
+  gem 'shoulda', '~> 3.5', '>= 3.5.0'
   gem "rdoc", "~> 3.12"
+  gem 'jeweler', '~> 1.8', '>= 1.8.3'
+  gem 'bundler', '~> 1.6', '>= 1.6.2'
+  gem 'bio', '~> 1.4', '>= 1.4.2'
+  gem 'minitest', '~> 4.7', '>= 4.7.5'
 end
+

data/Rakefile

@@ -18,7 +18,7 @@ Jeweler::Tasks.new do |gem|
   gem.homepage = "http://github.com/wwood/bioruby-hmmer3_report"
   gem.license = "MIT"
   gem.summary = %Q{Enables parsing of HMMER version 3 reports}
-  gem.description = %Q{Enables parsing of HMMER version 3 reports}
+  gem.description = %Q{Enables programmatic parsing of HMMER version 3 reports}
   gem.email = "gmail.com after donttrustben"
   gem.authors = ["Christian Zmasek","Ben J Woodcroft"]
   # dependencies defined in Gemfile

data/VERSION

@@ -1 +1 @@
-0.0.1
+0.1.0

data/lib/bio-hmmer3_report.rb

@@ -1,2 +1,4 @@
-require 'bio/appl/hmmer/hmmer3/report'
+require 'bio-logger'
+Bio::Log::LoggerPlus.new('bio-hmmer3report')
 
+require 'bio/appl/hmmer/hmmer3/default_report'

data/lib/bio/appl/hmmer/hmmer3/default_report.rb

@@ -0,0 +1,226 @@
+
+require 'bio/appl/hmmer/hmmer3/tabular_report'
+
+
+module Bio
+  class HMMER
+    class HMMER3
+
+    def self.reports(multiple_report_text, options={})
+      if [:domtblout, :tblout].include?(options[:format])
+        return TabularReport.new(multiple_report_text, options[:format])
+      else
+        ary = []
+        multiple_report_text.each_line("\n//\n") do |report|
+          if block_given?
+            yield DefaultHMMSearchReport.new(report)
+          else
+            ary << DefaultHMMSearchReport.new(report)
+          end
+        end
+        return ary
+      end
+    end
+
+    # This class is for parsing HMMSearch outputs from the default output
+    class DefaultHMMSearchReport
+      # Delimiter of each entry for Bio::FlatFile support.
+      DELIMITER = RS = "\n//\n"
+
+      def initialize(data)
+        # The input data is divided into chunks, a hash called @report_chunks (previously called subdata)
+        @report_chunks = get_subdata(data)
+        
+        @log = Bio::Log::LoggerPlus['bio-hmmer3report']
+      end
+  
+      # Return the report split up into chunks, so that those chunks can be further
+      # processed. Chunks are returned as a hash
+      def get_subdata(data)
+        subdata = {}
+        header_prefix = '\Ahmmsearch :: search' ## # hmmsearch :: search profile(s) against a sequence database
+        query_prefix  = '^Query:' ## Query:       2-Hacid_dh  [M=133]
+        hit_prefix    = '^Scores for complete sequences' ## Scores for complete sequences (score includes all domains):
+        aln_prefix    = '^Domain annotation for each sequence' ## Domain annotation for each sequence (and alignments):
+        stat_prefix   = '^\nInternal pipeline statistics summary:' ## Internal pipeline statistics summary:
+  
+        # if header exists, get it. Header only occurs in the first report
+        if data =~ /#{header_prefix}/
+          subdata["header"] = data[/(\A.+?)(?=#{query_prefix})/m]
+        end
+  
+        # split rest of report into sub-sections
+        subdata["query"] =      data[/(#{query_prefix}.+?)(?=#{hit_prefix})/m]
+        subdata["hit"] =        data[/(#{hit_prefix}.+?)(?=#{aln_prefix})/m]
+        subdata["alignment"] =  data[/(#{aln_prefix}.+?)(?=#{stat_prefix})/m]
+        subdata["statistics"] = data[/(#{stat_prefix}.+)\z/m]
+
+        return subdata
+      end
+      private :get_subdata
+      
+      # Parse the Query:, Accession: and :Description parts of the 
+      def parse_query
+        @report_chunks['query'].each_line do |line|
+          splits = line.split(':')
+          raise "Unexpected form of query header found in hmmsearch query chunk #{line.inspect}" unless splits.length>1
+          key = splits[0]
+          value = splits[1..(splits.length-1)].join(':').strip #in case there is colons in the value itself
+          
+          if key == 'Query'
+            @query = value
+          elsif key == 'Accession'
+            @query_accession = value
+          elsif key == 'Description'
+            @query_description = value
+          else
+            raise "Unexpected form of query header found in hmmsearch query chunk #{line.inspect}"
+          end
+        end
+      end
+      private :parse_query
+
+      def query
+        return @query unless @query.nil?
+        parse_query
+        return @query
+      end
+      
+      def query_accession
+        return @query_accession unless @query_accession.nil?
+        parse_query
+        return @query_accession
+      end
+      
+      def query_description
+        return @query_description unless @query_description.nil?
+        parse_query
+        return @query_description
+      end
+      
+      # TODO: parse statistical information
+      
+      # TODO: parse sequence-wise hits 
+      # (these can be derived from the domain_hits i.e. #hits, mind you, so ..). 
+      # Ah, actually in rare cases when this happens that isn't true: 
+      # "  [No individual domains that satisfy reporting thresholds (although complete target did)]"
+      
+      # Return an array of HMMER3::Hit objects from this report
+      def hits
+        return [] unless @report_chunks['alignment'].match(/^>>/)
+        # For each hit sequence (hits)
+        sequence_annotations = @report_chunks['alignment'].split(">>")
+        # puts "Found #{sequence_annotations.length} different hits e.g. #{sequence_annotations[0]}\n\n and #{sequence_annotations[1]} and \n\n #{sequence_annotations[sequence_annotations.length-1]}"
+        
+        alignments = []
+        sequence_annotations.each_with_index do |seq_annot, i|
+          #Ignore the first split as it is rubbish leftover from the split above
+          next if i==0
+          
+          # Now split on \n\n. Each of these splits should have 1 or more domains associated
+          
+          #First of this split will be "stanzas" like this
+          #>> 637984252  Acid345_2236 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding [Korebacter versatilis Ellin345]
+          #   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+          # ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+          #   1 !  120.2   0.5   7.6e-39   1.2e-35       1     133 []       3     313 ..       3     313 .. 0.98
+          
+          #And AFTER the first split comes "stanzas" like this
+          #  Alignments for each domain:
+          #  == domain 1    score: 120.2 bits;  conditional E-value: 7.6e-39
+          #                 EEECST.-CCHHHHHCC..TEEEEEEC.GSSHHHHHC....-SEEEE-TTS-BSHHHHCC-TT--EEEES----TTB-HHHHHH---EEE--TTTTHHH CS
+          #                 xxxxxxxxxxxxxxxxx..xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+          #  2-Hacid_dh   1 vlileplreeelellke..gvevevkd.ellteellekakdadalivrsntkvtaevleklpkLkviatagvGvDniDldaakerGIlVtnvpgystes 96 
+          #                 +++ e++ +++++l+k+    +v++ d   ++e+lle++k+adalivrs   v+a++le++ +L+vi++agvGvDni l+aa+++GI+V+n+pg+++ +
+          #   637982115   3 IVVAEKIAKAAIDLFKQdpTWNVVTPDqVAQKEQLLEQLKGADALIVRSAVFVDAAMLEHADQLRVIGRAGVGVDNIELEAATRKGIAVMNTPGANAIA 101
+          #                 6889999**********8544777777778888****************************************************************** PP
+          stanzas = seq_annot.split("\n\n")
+          
+          hit = Hit.new
+          hsps = []
+          
+          # Parse the first
+          lines = stanzas[0].split("\n")
+          sequence_name = lines[0].gsub(/^ /,'')
+          hit.sequence_name = sequence_name
+          
+          @log.debug "Now parsing table for #{sequence_name}"
+          return [] if lines[1].match(/^   \[No individual domains that/)
+
+          lines[3..(lines.length-1)].each do |line|
+            annotation = Hit::Hsp.new
+            
+            splits = line.split(/\s+/)
+            i = 1
+            annotation.number = splits[i].to_i; i+=2
+            annotation.score = splits[i].to_f; i+=1
+            annotation.bias = splits[i].to_f; i+=1
+            annotation.c_evalue = splits[i].to_f; i+=1
+            annotation.i_evalue = splits[i].to_f; i+=1
+            annotation.hmmfrom = splits[i].to_i; i+=1
+            annotation.hmm_to = splits[i].to_i; i+=2
+            annotation.alifrom = splits[i].to_i; i+=1
+            annotation.ali_to = splits[i].to_i; i+=2
+            annotation.envfrom = splits[i].to_i; i+=1
+            annotation.env_to = splits[i].to_i; i+=2
+            annotation.acc = splits[i].to_f
+            hsps.push annotation
+          end
+          
+          # Parse the second stanza and beyond
+          current_hsp = nil
+          (1..(stanzas.length-1)).each_with_index do |aln, index|
+            next if stanzas[aln] == "\n"
+            stanza = stanzas[aln].split("\n")
+            line_offset = 0
+            line_offset += 1 if index==0 #to account for the "Alignments for each domain:" line
+            # Is this a new HSP being described?
+            if matches = stanza[line_offset].match(/^  == domain (\d+)/)
+              domain_index = matches[1].to_i-1
+              current_hsp = hsps[domain_index]
+              line_offset += 1 # to account for the "== domain 1    score: 26.8 bits;  conditional E-value: 5.7e-10" line
+            end
+            
+            # Detect CS and RF lines
+            line_offset += 1 if stanza[line_offset].split(/\s+/)[2] == 'CS'
+            line_offset += 1 if stanza[line_offset].split(/\s+/)[2] == 'RF'
+            
+            # Add the lines to the relevant places
+            current_hsp.hmmseq ||= ''
+            current_hsp.hmmseq += stanza[line_offset].split(/\s+/)[3]
+            current_hsp.flatseq ||= ''
+            current_hsp.flatseq += stanza[2+line_offset].split(/\s+/)[3]
+          end
+          
+          hit.hsps = hsps
+          alignments.push hit
+          
+          @log.debug "Parsed alignments for sequence #{hit.sequence_name}" if @log.debug?
+        end
+        
+        return alignments
+      end
+      
+      # TODO: There is some overlapping code here between the tabular report Hit object and this object, probably should DRY it up a bit.
+      class Hit
+        attr_accessor :sequence_name
+        
+        attr_accessor :hsps
+        
+        def initialise
+          @hsps = []
+        end
+        
+        class Hsp
+          attr_accessor :number, :score, :bias, :c_evalue, :i_evalue, :hmmfrom, :hmm_to, :alifrom, :ali_to, :envfrom, :env_to, :acc
+        
+          attr_accessor :hmmseq, :flatseq
+        end # class DomainHitAnnotation
+      end # class DomainHitAnnotation
+      
+      end #class DefaultHMMSearchReport
+    end # class HMMER3
+
+  end # class HMMER
+
+end # module Bio

data/lib/bio/appl/hmmer/hmmer3/{report.rb → tabular_report.rb}

@@ -16,7 +16,7 @@ module Bio
     #
     # Parser class for hmmsearch and hmmscan in the HMMER 3 package. See README of this biogem for more information.
     class HMMER3
-      class Report
+      class TabularReport
         def initialize(hmmer_output, format = nil)
           
           @hits = Array.new

data/test/data/HMMER/hmmer3_onlyWholeSequenceNotDomains.txt

@@ -0,0 +1,39 @@
+# hmmsearch :: search profile(s) against a sequence database
+# HMMER 3.0 (March 2010); http://hmmer.org/
+# Copyright (C) 2010 Howard Hughes Medical Institute.
+# Freely distributed under the GNU General Public License (GPLv3).
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# query HMM file:                  /srv/whitlam/bio/db/pfam/26/Pfam-A.hmm
+# target sequence database:        /srv/whitlam/bio/db/img/3.5/genomes/finished//637000007/637000007.genes.faa
+# model-specific thresholding:     TC cutoffs
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+Query:       3Beta_HSD  [M=280]
+Accession:   PF01073.14
+Description: 3-beta hydroxysteroid dehydrogenase/isomerase family
+Scores for complete sequences (score includes all domains):
+   --- full sequence ---   --- best 1 domain ---    -#dom-
+    E-value  score  bias    E-value  score  bias    exp  N  Sequence  Description
+    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
+    1.8e-06   25.1   0.0     0.0051   13.8   0.2    3.0  0  637862688 Adeh_1165 Long-chain-fatty-acid CoA ligase [Anaero
+
+
+Domain annotation for each sequence (and alignments):
+>> 637862688  Adeh_1165 Long-chain-fatty-acid CoA ligase [Anaeromyxobacter dehalogenans 2CP-C]
+   [No individual domains that satisfy reporting thresholds (although complete target did)]
+
+
+
+Internal pipeline statistics summary:
+-------------------------------------
+Query model(s):                            1  (280 nodes)
+Target sequences:                       4361  (1522812 residues)
+Passed MSV filter:                       103  (0.0236184); expected 87.2 (0.02)
+Passed bias filter:                      102  (0.0233891); expected 87.2 (0.02)
+Passed Vit filter:                        43  (0.00986012); expected 4.4 (0.001)
+Passed Fwd filter:                        28  (0.00642055); expected 0.0 (1e-05)
+Initial search space (Z):               4361  [actual number of targets]
+Domain search space  (domZ):              22  [number of targets reported over threshold]
+# CPU time: 0.29u 0.04s 00:00:00.32 Elapsed: 00:00:00.14
+# Mc/sec: 3045.62
+//

data/test/data/HMMER/hmmer3multidomainHit.txt

@@ -0,0 +1,100 @@
+# hmmsearch :: search profile(s) against a sequence database
+# HMMER 3.0 (March 2010); http://hmmer.org/
+# Copyright (C) 2010 Howard Hughes Medical Institute.
+# Freely distributed under the GNU General Public License (GPLv3).
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# query HMM file:                  /srv/whitlam/bio/db/pfam/26/Pfam-A.hmm
+# target sequence database:        /srv/whitlam/bio/db/img/3.5/genomes/finished//637000001/637000001.genes.faa
+# model-specific thresholding:     TC cutoffs
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+Query:       3HCDH  [M=97]
+Accession:   PF00725.17
+Description: 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
+Scores for complete sequences (score includes all domains):
+   --- full sequence ---   --- best 1 domain ---    -#dom-
+    E-value  score  bias    E-value  score  bias    exp  N  Sequence  Description
+    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
+    1.7e-36  122.8   0.0    3.6e-36  121.8   0.0    1.6  1  637983221 Acid345_1212 3-hydroxybutyryl-CoA dehydrogenase [K
+    2.4e-36  122.4   0.1    8.3e-36  120.7   0.0    1.9  1  637986361 Acid345_4328 3-hydroxybutyryl-CoA dehydrogenase [K
+    5.7e-24   82.7   0.1    1.3e-14   52.7   0.0    3.4  2  637984486 Acid345_2469 3-hydroxyacyl-CoA dehydrogenase, NAD-
+    5.3e-20   70.0   0.0    1.2e-19   68.8   0.0    1.6  1  637984778 Acid345_2761 3-hydroxybutyryl-CoA dehydrogenase [K
+
+
+Domain annotation for each sequence (and alignments):
+>> 637983221  Acid345_1212 3-hydroxybutyryl-CoA dehydrogenase [Korebacter versatilis Ellin345]
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !  121.8   0.0     3e-39   3.6e-36       1      97 []     185     281 ..     185     281 .. 1.00
+
+  Alignments for each domain:
+  == domain 1    score: 121.8 bits;  conditional E-value: 3e-39
+                ---HHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHH.-------HHHHHH---HHHHHHHHHHHCTCCCHGG-..HHHHHHHHTT-----------EC CS
+      3HCDH   1 GFvvnRvlapllneairlveegvatpediDaamkkglGlpmGpfelsdlvgldvakkilevlaeelgerayapsplleklveagrlgrktgkgfyky 97 
+                GF+vnR+l+p+l +air +eegv ++ diD+amk+g+G+pmGpf+l+d vgld++++i++v+ +e+ e+++a++pll+++v ag +grktgkgfy+y
+  637983221 185 GFIVNRLLVPYLLDAIRAYEEGVGSIVDIDQAMKLGCGYPMGPFTLLDFVGLDTCYYITHVMFDEFREKRFAAPPLLKRMVLAGWYGRKTGKGFYDY 281
+                9**********************************************************************************************99 PP
+
+>> 637986361  Acid345_4328 3-hydroxybutyryl-CoA dehydrogenase [Korebacter versatilis Ellin345]
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !  120.7   0.0     7e-39   8.3e-36       1      97 []     186     282 .]     186     282 .] 1.00
+
+  Alignments for each domain:
+  == domain 1    score: 120.7 bits;  conditional E-value: 7e-39
+                ---HHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHH.-------HHHHHH---HHHHHHHHHHHCTCCCHGG-..HHHHHHHHTT-----------EC CS
+      3HCDH   1 GFvvnRvlapllneairlveegvatpediDaamkkglGlpmGpfelsdlvgldvakkilevlaeelgerayapsplleklveagrlgrktgkgfyky 97 
+                GFv nRvl+pllnea+  v egvatpe +D+++k+g+ +pmGp++l+d +gldv+ +i++vl+ +lg+++y+p+pll k+v+ag lgrk+g+gfyky
+  637986361 186 GFVSNRVLMPLLNEAMYAVMEGVATPEAVDEVFKLGMAHPMGPLTLADFIGLDVCLDIMRVLQTGLGDPKYRPCPLLIKMVDAGWLGRKSGRGFYKY 282
+                9***********************************************************************************************9 PP
+
+>> 637984486  Acid345_2469 3-hydroxyacyl-CoA dehydrogenase, NAD-binding [Korebacter versatilis Ellin345]
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   52.7   0.0   1.1e-17   1.3e-14       2      96 ..     196     293 ..     196     294 .. 0.97
+   2 !   25.6   0.0   3.2e-09   3.8e-06      24      61 ..     378     415 ..     359     435 .. 0.78
+
+  Alignments for each domain:
+  == domain 1    score: 52.7 bits;  conditional E-value: 1.1e-17
+                --HHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHH.----.---HHHHHH---HHHHHHHHHHHCTCCCH..GG-..HHHHHHHHTT-----------E CS
+      3HCDH   2 FvvnRvlapllneairlveegvatpediDaamkkglGlp.mGpfelsdlvgldvakkilevlaeelger..ayapsplleklveagrlgrktgkgfyk 96 
+                F+ nR+    + ++ir+++e  +++ed+Da++  ++G+p  ++f+++dlvgld+  ++   +++  +++  + + +++ ++++e + lg kt+ gfyk
+  637984486 196 FIGNRIGTFSVLNVIRVMQEMDLSIEDVDALTGSAVGWPkSATFRTIDLVGLDILGHVVGNMKQNVTDErsDLQIPDFYKQMLERKWLGDKTKGGFYK 293
+                9**************************************999******************999999999899999**********************8 PP
+
+  == domain 2    score: 25.6 bits;  conditional E-value: 3.2e-09
+                S-HHHHHHHHHH.-------HHHHHH---HHHHHHHHH CS
+      3HCDH  24 atpediDaamkkglGlpmGpfelsdlvgldvakkilev 61 
+                 t+ +iDaam+ g+++ mGpfel d +g+++    +++
+  637984486 378 DTIVEIDAAMRMGFNWEMGPFELWDAAGVEATVGRMKA 415
+                5789*************************998877763 PP
+
+>> 637984778  Acid345_2761 3-hydroxybutyryl-CoA dehydrogenase [Korebacter versatilis Ellin345]
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   68.8   0.0     1e-22   1.2e-19       3      85 ..     190     271 ..     188     275 .. 0.96
+
+  Alignments for each domain:
+  == domain 1    score: 68.8 bits;  conditional E-value: 1e-22
+                -HHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHH.-------HHHHHH---HHHHHHHHHHHCTCCCHGG-..HHHHHHHHTT- CS
+      3HCDH   3 vvnRvlapllneairlveegvatpediDaamkkglGlpmGpfelsdlvgldvakkilevlaeelgerayapsplleklveagr 85 
+                ++ R++a + nea++++ eg a++e+iD+a+++glGlpmGp++ ++ +gl+   +++e+l+++lge+ y+p+plle++v+a++
+  637984778 190 ITARMQALISNEAFKMLGEGLASAEEIDRALQQGLGLPMGPIAEAEQYGLERRLRMMEYLHKTLGET-YRPAPLLEQYVKANK 271
+                899***************************************************************9.899*********986 PP
+
+
+
+Internal pipeline statistics summary:
+-------------------------------------
+Query model(s):                            1  (97 nodes)
+Target sequences:                       4779  (1680477 residues)
+Passed MSV filter:                       142  (0.0297133); expected 95.6 (0.02)
+Passed bias filter:                      122  (0.0255284); expected 95.6 (0.02)
+Passed Vit filter:                        12  (0.00251099); expected 4.8 (0.001)
+Passed Fwd filter:                         4  (0.000836995); expected 0.0 (1e-05)
+Initial search space (Z):               4779  [actual number of targets]
+Domain search space  (domZ):               4  [number of targets reported over threshold]
+# CPU time: 0.09u 0.01s 00:00:00.10 Elapsed: 00:00:00.05
+# Mc/sec: 3260.13
+//
+

data/test/data/HMMER/hmmer3multidomainHitSimple.txt

@@ -0,0 +1,58 @@
+# hmmsearch :: search profile(s) against a sequence database
+# HMMER 3.0 (March 2010); http://hmmer.org/
+# Copyright (C) 2010 Howard Hughes Medical Institute.
+# Freely distributed under the GNU General Public License (GPLv3).
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# query HMM file:                  /srv/whitlam/bio/db/pfam/26/Pfam-A.hmm
+# target sequence database:        /srv/whitlam/bio/db/img/3.5/genomes/finished//637000001/637000001.genes.faa
+# model-specific thresholding:     TC cutoffs
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+Query:       3HCDH  [M=97]
+Accession:   PF00725.17
+Description: 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
+Scores for complete sequences (score includes all domains):
+   --- full sequence ---   --- best 1 domain ---    -#dom-
+    E-value  score  bias    E-value  score  bias    exp  N  Sequence  Description
+    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
+    5.7e-24   82.7   0.1    1.3e-14   52.7   0.0    3.4  2  637984486 Acid345_2469 3-hydroxyacyl-CoA dehydrogenase, NAD-
+
+
+Domain annotation for each sequence (and alignments):
+>> 637984486  Acid345_2469 3-hydroxyacyl-CoA dehydrogenase, NAD-binding [Korebacter versatilis Ellin345]
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   52.7   0.0   1.1e-17   1.3e-14       2      96 ..     196     293 ..     196     294 .. 0.97
+   2 !   25.6   0.0   3.2e-09   3.8e-06      24      61 ..     378     415 ..     359     435 .. 0.78
+
+  Alignments for each domain:
+  == domain 1    score: 52.7 bits;  conditional E-value: 1.1e-17
+                --HHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHH.----.---HHHHHH---HHHHHHHHHHHCTCCCH..GG-..HHHHHHHHTT-----------E CS
+      3HCDH   2 FvvnRvlapllneairlveegvatpediDaamkkglGlp.mGpfelsdlvgldvakkilevlaeelger..ayapsplleklveagrlgrktgkgfyk 96 
+                F+ nR+    + ++ir+++e  +++ed+Da++  ++G+p  ++f+++dlvgld+  ++   +++  +++  + + +++ ++++e + lg kt+ gfyk
+  637984486 196 FIGNRIGTFSVLNVIRVMQEMDLSIEDVDALTGSAVGWPkSATFRTIDLVGLDILGHVVGNMKQNVTDErsDLQIPDFYKQMLERKWLGDKTKGGFYK 293
+                9**************************************999******************999999999899999**********************8 PP
+
+  == domain 2    score: 25.6 bits;  conditional E-value: 3.2e-09
+                S-HHHHHHHHHH.-------HHHHHH---HHHHHHHHH CS
+      3HCDH  24 atpediDaamkkglGlpmGpfelsdlvgldvakkilev 61 
+                 t+ +iDaam+ g+++ mGpfel d +g+++    +++
+  637984486 378 DTIVEIDAAMRMGFNWEMGPFELWDAAGVEATVGRMKA 415
+                5789*************************998877763 PP
+
+
+
+Internal pipeline statistics summary:
+-------------------------------------
+Query model(s):                            1  (97 nodes)
+Target sequences:                       4779  (1680477 residues)
+Passed MSV filter:                       142  (0.0297133); expected 95.6 (0.02)
+Passed bias filter:                      122  (0.0255284); expected 95.6 (0.02)
+Passed Vit filter:                        12  (0.00251099); expected 4.8 (0.001)
+Passed Fwd filter:                         4  (0.000836995); expected 0.0 (1e-05)
+Initial search space (Z):               4779  [actual number of targets]
+Domain search space  (domZ):               4  [number of targets reported over threshold]
+# CPU time: 0.09u 0.01s 00:00:00.10 Elapsed: 00:00:00.05
+# Mc/sec: 3260.13
+//
+

data/test/data/HMMER/test637000001.hmmsearch.txt

@@ -0,0 +1,209 @@
+# hmmsearch :: search profile(s) against a sequence database
+# HMMER 3.0 (March 2010); http://hmmer.org/
+# Copyright (C) 2010 Howard Hughes Medical Institute.
+# Freely distributed under the GNU General Public License (GPLv3).
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+# query HMM file:                  /srv/whitlam/bio/db/pfam/26/Pfam-A.hmm
+# target sequence database:        /srv/whitlam/bio/db/img/3.5/genomes/finished//637000001/637000001.genes.faa
+# model-specific thresholding:     TC cutoffs
+# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
+
+Query:       1-cysPrx_C  [M=40]
+Accession:   PF10417.4
+Description: C-terminal domain of 1-Cys peroxiredoxin
+Scores for complete sequences (score includes all domains):
+   --- full sequence ---   --- best 1 domain ---    -#dom-
+    E-value  score  bias    E-value  score  bias    exp  N  Sequence Description
+    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
+
+   [No hits detected that satisfy reporting thresholds]
+
+
+Domain annotation for each sequence (and alignments):
+
+   [No targets detected that satisfy reporting thresholds]
+
+
+Internal pipeline statistics summary:
+-------------------------------------
+Query model(s):                            1  (40 nodes)
+Target sequences:                       4779  (1680477 residues)
+Passed MSV filter:                       169  (0.035363); expected 95.6 (0.02)
+Passed bias filter:                      142  (0.0297133); expected 95.6 (0.02)
+Passed Vit filter:                        10  (0.00209249); expected 4.8 (0.001)
+Passed Fwd filter:                         1  (0.000209249); expected 0.0 (1e-05)
+Initial search space (Z):               4779  [actual number of targets]
+Domain search space  (domZ):               0  [number of targets reported over threshold]
+# CPU time: 0.09u 0.01s 00:00:00.10 Elapsed: 00:00:00.06
+# Mc/sec: 1120.32
+//
+Query:       120_Rick_ant  [M=255]
+Accession:   PF12574.3
+Description: 120 KDa Rickettsia surface antigen
+Scores for complete sequences (score includes all domains):
+   --- full sequence ---   --- best 1 domain ---    -#dom-
+    E-value  score  bias    E-value  score  bias    exp  N  Sequence Description
+    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
+
+   [No hits detected that satisfy reporting thresholds]
+
+
+Domain annotation for each sequence (and alignments):
+
+   [No targets detected that satisfy reporting thresholds]
+
+
+Internal pipeline statistics summary:
+-------------------------------------
+Query model(s):                            1  (255 nodes)
+Target sequences:                       4779  (1680477 residues)
+Passed MSV filter:                       109  (0.0228081); expected 95.6 (0.02)
+Passed bias filter:                       92  (0.0192509); expected 95.6 (0.02)
+Passed Vit filter:                         6  (0.00125549); expected 4.8 (0.001)
+Passed Fwd filter:                         0  (0); expected 0.0 (1e-05)
+Initial search space (Z):               4779  [actual number of targets]
+Domain search space  (domZ):               0  [number of targets reported over threshold]
+# CPU time: 0.12u 0.02s 00:00:00.13 Elapsed: 00:00:00.05
+# Mc/sec: 8570.43
+//
+Query:       14-3-3  [M=236]
+Accession:   PF00244.15
+Description: 14-3-3 protein
+Scores for complete sequences (score includes all domains):
+   --- full sequence ---   --- best 1 domain ---    -#dom-
+    E-value  score  bias    E-value  score  bias    exp  N  Sequence Description
+    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
+
+   [No hits detected that satisfy reporting thresholds]
+
+
+Domain annotation for each sequence (and alignments):
+
+   [No targets detected that satisfy reporting thresholds]
+
+
+Internal pipeline statistics summary:
+-------------------------------------
+Query model(s):                            1  (236 nodes)
+Target sequences:                       4779  (1680477 residues)
+Passed MSV filter:                       150  (0.0313873); expected 95.6 (0.02)
+Passed bias filter:                       96  (0.0200879); expected 95.6 (0.02)
+Passed Vit filter:                         4  (0.000836995); expected 4.8 (0.001)
+Passed Fwd filter:                         0  (0); expected 0.0 (1e-05)
+Initial search space (Z):               4779  [actual number of targets]
+Domain search space  (domZ):               0  [number of targets reported over threshold]
+# CPU time: 0.12u 0.03s 00:00:00.15 Elapsed: 00:00:00.07
+# Mc/sec: 5665.61
+//
+Query:       2-Hacid_dh  [M=133]
+Accession:   PF00389.25
+Description: D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
+Scores for complete sequences (score includes all domains):
+   --- full sequence ---   --- best 1 domain ---    -#dom-
+    E-value  score  bias    E-value  score  bias    exp  N  Sequence  Description
+    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
+    6.2e-36  121.1   2.3    1.2e-35  120.2   0.5    2.2  1  637982115 Acid345_0115 D-3-phosphoglycerate dehydrogenase [K
+      3e-19   67.1   0.0    3.8e-19   66.8   0.0    1.3  1  637984252 Acid345_2236 D-isomer specific 2-hydroxyacid dehyd
+    6.2e-07   27.3   0.0      9e-07   26.8   0.0    1.3  1  637983083 Acid345_1074 D-isomer specific 2-hydroxyacid dehyd
+
+
+Domain annotation for each sequence (and alignments):
+>> 637982115  Acid345_0115 D-3-phosphoglycerate dehydrogenase [Korebacter versatilis Ellin345]
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !  120.2   0.5   7.6e-39   1.2e-35       1     133 []       3     313 ..       3     313 .. 0.98
+
+  Alignments for each domain:
+  == domain 1    score: 120.2 bits;  conditional E-value: 7.6e-39
+                 EEECST.-CCHHHHHCC..TEEEEEEC.GSSHHHHHC....-SEEEE-TTS-BSHHHHCC-TT--EEEES----TTB-HHHHHH---EEE--TTTTHHH CS
+                 xxxxxxxxxxxxxxxxx..xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  2-Hacid_dh   1 vlileplreeelellke..gvevevkd.ellteellekakdadalivrsntkvtaevleklpkLkviatagvGvDniDldaakerGIlVtnvpgystes 96 
+                 +++ e++ +++++l+k+    +v++ d   ++e+lle++k+adalivrs   v+a++le++ +L+vi++agvGvDni l+aa+++GI+V+n+pg+++ +
+   637982115   3 IVVAEKIAKAAIDLFKQdpTWNVVTPDqVAQKEQLLEQLKGADALIVRSAVFVDAAMLEHADQLRVIGRAGVGVDNIELEAATRKGIAVMNTPGANAIA 101
+                 6889999**********8544777777778888****************************************************************** PP
+
+                 HHHHH.............................................................................................. CS
+                 xxxxx.............................................................................................. RF
+  2-Hacid_dh  97 vAEla.............................................................................................. 101
+                 vAE++                                                                                              
+   637982115 102 VAEHTiglmlalarfipratetmhagkwekkslqgtelrgktlgivglgriglevarraasfgmtlvahdpyvspaiahdakirladrdevlavadyit 200
+                 *************************************************************************************************** PP
+
+                 .................................................................................T-CHHHHHHHHHHHHHHH CS
+                 .................................................................................xxxxxxxxxxxxxxxxxx RF
+  2-Hacid_dh 102 .................................................................................fateeaqenmaeeaaenl 119
+                                                                                                  ++t eaq++++ ++a ++
+   637982115 201 lhvgltpqtanminattlatmkkgvrivncargeliddaalaeavksghvggaaldvfteeplkaspyhgvpnviltphigGSTAEAQDAVGVQIAHQV 299
+                 *************************************************************************************************** PP
+
+                 HHHH--G--TCCE- CS
+                 xxxxxxxxxxxxxx RF
+  2-Hacid_dh 120 vaflkgespanavn 133
+                 +++l+ + ++navn
+   637982115 300 RDYLQRGVVQNAVN 313
+                 *************8 PP
+
+>> 637984252  Acid345_2236 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding [Korebacter versatilis Ellin345]
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   66.8   0.0   2.4e-22   3.8e-19       7     102 ..      14     146 ..       8     353 .. 0.77
+
+  Alignments for each domain:
+  == domain 1    score: 66.8 bits;  conditional E-value: 2.4e-22
+                 .-CCHHHHHCC.TEEEEEEC...GSSHHHHHC.....-SEEEE-TTS-BSHHHHCC-.TT--EEEES----TTB-HHHHHH---EEE--TTTTHHHHHH CS
+                 xxxxxxxxxxx.xxxxxxxx...xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  2-Hacid_dh   7 lreeelellke.gvevevkd...ellteellekakd.adalivrsntkvtaevlekl.pkLkviatagvGvDniDldaakerGIlVtnvpgystesvAE 99 
+                 + + +le+l++ g++vev+     ++++ ++ek++  +d+li++ ++k++aev+e+   +Lkv+a+++vG+Dni+ + a+++ +  t++ +++te++AE
+   637984252  14 IGKPALERLRAaGYDVEVYPqadPPPKSLIIEKVASgIDGLITTLRDKIDAEVFEAGkGNLKVVAQIAVGFDNINRADANKYKVPFTHTADVLTEATAE 112
+                 55667788888888*****999766667667776655********************9***************************************** PP
+
+                 HH...............................T CS
+                 xx...............................x RF
+  2-Hacid_dh 100 la...............................f 102
+                 +a                               f
+   637984252 113 FAffimaaaarklwtaernvrdlkwgtwhpflpF 146
+                 **66666555555555555555555555555550 PP
+
+>> 637983083  Acid345_1074 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding [Korebacter versatilis Ellin345]
+   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
+ ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
+   1 !   26.8   0.0   5.7e-10     9e-07      30     132 ..      40     321 ..      18     322 .. 0.89
+
+  Alignments for each domain:
+  == domain 1    score: 26.8 bits;  conditional E-value: 5.7e-10
+                 HHHHC....-SEEEE-TTS-BSHHHHCC-TT--EEEES----TTB-HHHHHH---EEE--TTTTHHHHHHHH........................... CS
+                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................... RF
+  2-Hacid_dh  30 eellekakdadalivrsntkvtaevleklpkLkviatagvGvDniDldaakerGIlVtnvpgystesvAEla........................... 101
+                 ++l ++++dad+ ++r  +      + ++++Lk+i  a++ v  + +  +++ +I+Vtn+ ++    vAE+a                           
+   637983083  40 ATLEQEISDADIALTRELK---PSQVHAAKQLKWIHSAAAAVHALMIPEIRQSNIIVTNATAVHGPVVAEHAlamilaiarridlavkaqtehiwkqee 135
+                 5677888888888888755...7778899********************************************************************** PP
+
+                 ................................................................................................... CS
+                 ................................................................................................... RF
+  2-Hacid_dh 102 ................................................................................................... 101
+                                                                                                                    
+   637983083 136 iwvtnppprdiagstllvvglgqigrplaqkakalgmhviavrehpergaetadevfaskdllkilpradfvmlcppvtpdtkeafgrdqlaamkpday 234
+                 *99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 PP
+
+                 ........................................................T-CHHHHHHHHHHHHHHHHHHH--G--TCCE CS
+                 ........................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+  2-Hacid_dh 102 ........................................................fateeaqenmaeeaaenlvaflkgespanav 132
+                                                                         + + +  e+    + enl++fl+g+++   v
+   637983083 235 llnvgrgalidepaliealqqrriggaaldvtsveplpsdsplwaldncmitphtgGISPKLWERQYIFFTENLRRFLAGKPLLGLV 321
+                 999999999999999999999999999999999999999999999999999999998888888888888888888888888776655 PP
+
+
+
+Internal pipeline statistics summary:
+-------------------------------------
+Query model(s):                            1  (133 nodes)
+Target sequences:                       4779  (1680477 residues)
+Passed MSV filter:                       187  (0.0391295); expected 95.6 (0.02)
+Passed bias filter:                      167  (0.0349445); expected 95.6 (0.02)
+Passed Vit filter:                        22  (0.00460347); expected 4.8 (0.001)
+Passed Fwd filter:                         3  (0.000627746); expected 0.0 (1e-05)
+Initial search space (Z):               4779  [actual number of targets]
+Domain search space  (domZ):               3  [number of targets reported over threshold]
+# CPU time: 0.13u 0.00s 00:00:00.13 Elapsed: 00:00:00.07
+# Mc/sec: 3192.91
+//

data/test/helper.rb

@@ -8,11 +8,12 @@ rescue Bundler::BundlerError => e
   exit e.status_code
 end
 require 'test/unit'
-require 'shoulda'
+
 
 $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
 $LOAD_PATH.unshift(File.dirname(__FILE__))
 require 'bio-hmmer3_report'
 
 class Test::Unit::TestCase
+  HMMER_TEST_DATA = Pathname.new(File.join('test','data','HMMER')).cleanpath.to_s
 end

data/test/unit/bio/appl/hmmer/test_hmmer3_default_report.rb

@@ -0,0 +1,84 @@
+require 'helper'
+
+module Bio
+  class TestDefaultReport < Test::Unit::TestCase
+    def test_splitting
+      reports = Bio::HMMER::HMMER3.reports(File.open(File.join(HMMER_TEST_DATA, 'test637000001.hmmsearch.txt')))
+      assert_equal 4, reports.length
+      assert_kind_of Bio::HMMER::HMMER3::DefaultHMMSearchReport, reports[0]
+    end
+    
+    def test_alignment_when_no_hits
+      reports = Bio::HMMER::HMMER3.reports(File.open(File.join(HMMER_TEST_DATA, 'test637000001.hmmsearch.txt')))
+      assert_equal [], reports[0].hits
+    end
+
+    def test_alignment_when_three_hits
+      reports = Bio::HMMER::HMMER3.reports(File.open(File.join(HMMER_TEST_DATA, 'test637000001.hmmsearch.txt')))
+      hits = reports[3].hits
+      assert_kind_of Array, hits
+      
+      assert_equal 3, hits.length
+      
+      
+      h = hits[1]
+      assert_kind_of Bio::HMMER::HMMER3::DefaultHMMSearchReport::Hit, h
+      assert_equal 1, h.hsps.length
+      assert_equal '637984252  Acid345_2236 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding [Korebacter versatilis Ellin345]',
+        h.sequence_name
+      
+      d = h.hsps[0]
+      assert_kind_of Bio::HMMER::HMMER3::DefaultHMMSearchReport::Hit::Hsp, d
+      assert_equal 1, d.number
+      assert_equal 66.8, d.score
+      assert_equal 0.0, d.bias
+      assert_equal 2.4e-22, d.c_evalue
+      assert_equal 3.8e-19, d.i_evalue
+      assert_equal 7, d.hmmfrom
+      assert_equal 102, d.hmm_to
+      assert_equal 14, d.alifrom
+      assert_equal 146, d.ali_to
+      assert_equal 8, d.envfrom
+      assert_equal 353, d.env_to
+      assert_equal 0.77, d.acc
+      
+      assert_equal 'lreeelellke.gvevevkd...ellteellekakd.adalivrsntkvtaevlekl.pkLkviatagvGvDniDldaakerGIlVtnvpgystesvAE'+
+        'la...............................f', d.hmmseq
+      assert_equal 'IGKPALERLRAaGYDVEVYPqadPPPKSLIIEKVASgIDGLITTLRDKIDAEVFEAGkGNLKVVAQIAVGFDNINRADANKYKVPFTHTADVLTEATAE'+
+        'FAffimaaaarklwtaernvrdlkwgtwhpflpF', d.flatseq
+        
+      assert_equal 'IVVAEKIAKAAIDLFKQdpTWNVVTPDqVAQKEQLLEQLKGADALIVRSAVFVDAAMLEHADQLRVIGRAGVGVDNIELEAATRKGIAVMNTPGANAIA'+
+        'VAEHTiglmlalarfipratetmhagkwekkslqgtelrgktlgivglgriglevarraasfgmtlvahdpyvspaiahdakirladrdevlavadyit'+
+        'lhvgltpqtanminattlatmkkgvrivncargeliddaalaeavksghvggaaldvfteeplkaspyhgvpnviltphigGSTAEAQDAVGVQIAHQV'+
+        'RDYLQRGVVQNAVN', hits[0].hsps[0].flatseq
+        
+      assert_equal 'eellekakdadalivrsntkvtaevleklpkLkviatagvGvDniDldaakerGIlVtnvpgystesvAEla...........................'+
+        '...................................................................................................'+
+        '........................................................fateeaqenmaeeaaenlvaflkgespanav', hits[2].hsps[0].hmmseq
+    end
+    
+    def test_multi_domain_hit_simple
+      hits = Bio::HMMER::HMMER3.reports(File.open(File.join(HMMER_TEST_DATA, 'hmmer3multidomainHitSimple.txt')))[0].hits
+      assert_equal 1, hits.length
+      assert_equal 2, hits[0].hsps.length
+      
+      assert_equal 'FIGNRIGTFSVLNVIRVMQEMDLSIEDVDALTGSAVGWPkSATFRTIDLVGLDILGHVVGNMKQNVTDErsDLQIPDFYKQMLERKWLGDKTKGGFYK', hits[0].hsps[0].flatseq
+      assert_equal 'DTIVEIDAAMRMGFNWEMGPFELWDAAGVEATVGRMKA', hits[0].hsps[1].flatseq
+    end
+    
+    def test_multi_domain_hit
+      hits = Bio::HMMER::HMMER3.reports(File.open(File.join(HMMER_TEST_DATA, 'hmmer3multidomainHit.txt')))[0].hits
+      assert_equal 4, hits.length
+      assert_equal 1, hits[0].hsps.length
+      assert_equal 2, hits[2].hsps.length
+      
+      assert_equal 'FIGNRIGTFSVLNVIRVMQEMDLSIEDVDALTGSAVGWPkSATFRTIDLVGLDILGHVVGNMKQNVTDErsDLQIPDFYKQMLERKWLGDKTKGGFYK', hits[2].hsps[0].flatseq
+      assert_equal 'DTIVEIDAAMRMGFNWEMGPFELWDAAGVEATVGRMKA', hits[2].hsps[1].flatseq
+    end
+    
+    def test_whole_sequence_only_not_individual_domains
+      assert_equal [],
+        Bio::HMMER::HMMER3.reports(File.open(File.join(HMMER_TEST_DATA, 'hmmer3_onlyWholeSequenceNotDomains.txt')))[0].hits
+    end
+  end
+end

data/test/unit/bio/appl/hmmer/test_hmmer3_report_formatting.rb

@@ -0,0 +1,24 @@
+require 'helper'
+
+module Bio
+  class TestDefaultReport < Test::Unit::TestCase
+    def test_no_format_specified
+      reports = Bio::HMMER::HMMER3.reports(File.open(File.join(HMMER_TEST_DATA, 'test637000001.hmmsearch.txt')))
+      assert_kind_of Array, reports
+      assert_equal 4, reports.length
+      assert_kind_of Bio::HMMER::HMMER3::DefaultHMMSearchReport, reports[0]
+    end
+    
+    def test_tblout_format_specified
+      report = Bio::HMMER::HMMER3.reports(File.open(File.join(HMMER_TEST_DATA, 'hmmsearch_tblout.out')), :format => :tblout)
+      assert_kind_of Bio::HMMER::HMMER3::TabularReport, report
+      assert_equal :tblout, report.format
+    end
+    
+    def test_domtblout_format_specified
+      report = Bio::HMMER::HMMER3.reports(File.open(File.join(HMMER_TEST_DATA, 'hmmsearch_domtblout.out')), :format => :domtblout)
+      assert_kind_of Bio::HMMER::HMMER3::TabularReport, report
+      assert_equal :domtblout, report.format
+    end
+  end
+end

data/test/unit/bio/appl/hmmer/test_hmmer3report.rb

@@ -10,40 +10,12 @@
 require 'helper'
 
 module Bio
-  module Testreport
-
-    HMMER_TEST_DATA = Pathname.new(File.join('test','data','HMMER')).cleanpath.to_s
-
-    def self.hmmsearch_domtblout_empty
-      File.open(File.join HMMER_TEST_DATA, 'hmmsearch_domtblout_empty.out')
-    end
-
-    def self.hmmsearch_domtblout
-      File.open(File.join HMMER_TEST_DATA, 'hmmsearch_domtblout.out')
-    end
-
-    def self.hmmsearch_tblout
-      File.open(File.join HMMER_TEST_DATA, 'hmmsearch_tblout.out')
-    end
-
-    def self.hmmscan_domtblout
-      File.open(File.join HMMER_TEST_DATA, 'hmmscan_domtblout.out')
-    end
-
-    def self.hmmscan_tblout
-      File.open(File.join HMMER_TEST_DATA, 'hmmscan_tblout.out')
-    end
-
-  end # Testreport
-
   class Testreport_class_methods < Test::Unit::TestCase
-
-
     def test_hmmsearch_domtblout_empty
-      filename = Testreport.hmmsearch_domtblout_empty
+      filename = File.open(File.join HMMER_TEST_DATA, 'hmmsearch_domtblout_empty.out')
 
-      assert_instance_of(Bio::HMMER::HMMER3::Report,
-        report = Bio::HMMER::HMMER3::Report.new(filename))
+      assert_instance_of(Bio::HMMER::HMMER3::TabularReport,
+        report = Bio::HMMER::HMMER3::TabularReport.new(filename))
 
       assert_instance_of(Array,
         report.hits)
@@ -53,10 +25,10 @@ module Bio
 
 
     def test_hmmsearch_domtblout
-      filename = Testreport.hmmsearch_domtblout
+      filename = File.open(File.join HMMER_TEST_DATA, 'hmmsearch_domtblout.out')
 
-      assert_instance_of(Bio::HMMER::HMMER3::Report,
-        report = Bio::HMMER::HMMER3::Report.new(filename))
+      assert_instance_of(Bio::HMMER::HMMER3::TabularReport,
+        report = Bio::HMMER::HMMER3::TabularReport.new(filename))
 
       assert_instance_of(Array,
         report.hits)
@@ -100,10 +72,10 @@ module Bio
 
     def test_hmmsearch_tblout
 
-      filename = Testreport.hmmsearch_tblout
+      filename = File.open(File.join HMMER_TEST_DATA, 'hmmsearch_tblout.out')
 
-      assert_instance_of(Bio::HMMER::HMMER3::Report,
-        report = Bio::HMMER::HMMER3::Report.new(filename))
+      assert_instance_of(Bio::HMMER::HMMER3::TabularReport,
+        report = Bio::HMMER::HMMER3::TabularReport.new(filename))
 
       assert_instance_of(Array,
         report.hits)
@@ -139,10 +111,10 @@ module Bio
 
     def test_hmmscan_domtblout
 
-      filename = Testreport.hmmscan_domtblout
+      filename = File.open(File.join HMMER_TEST_DATA, 'hmmscan_domtblout.out')
 
-      assert_instance_of(Bio::HMMER::HMMER3::Report,
-        report = Bio::HMMER::HMMER3::Report.new(filename))
+      assert_instance_of(Bio::HMMER::HMMER3::TabularReport,
+        report = Bio::HMMER::HMMER3::TabularReport.new(filename))
 
       assert_instance_of(Array,
         report.hits)
@@ -180,10 +152,10 @@ module Bio
     end # test_hmmscan_domtblout
 
     def test_hmmscan_tblout
-      filename = Testreport.hmmscan_tblout
+      filename = File.open(File.join HMMER_TEST_DATA, 'hmmscan_tblout.out')
 
-      assert_instance_of(Bio::HMMER::HMMER3::Report,
-        report = Bio::HMMER::HMMER3::Report.new(filename))
+      assert_instance_of(Bio::HMMER::HMMER3::TabularReport,
+        report = Bio::HMMER::HMMER3::TabularReport.new(filename))
 
       assert_instance_of(Array,
         report.hits)
@@ -225,7 +197,7 @@ module Bio
       data << "\n" << 'BH4                  PF02180.11    27 sp|P10415|BCL2_HUMAN -            239   3.9e-15   54.6   0.1   1   1   1.3e-18   8.2e-15   53.6   0.1     2    26     8    32     7    33 0.94 Bcl-2 homology region 4'
       data << "\n"
   
-      report = Bio::HMMER::HMMER3::Report.new(data)
+      report = Bio::HMMER::HMMER3::TabularReport.new(data)
       hits = report.hits
       hits.each do |hit|
         assert_kind_of Bio::HMMER::HMMER3::PerDomainHit, hit

metadata

@@ -1,8 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: bio-hmmer3_report
 version: !ruby/object:Gem::Version
-  version: 0.0.1
-  prerelease: 
+  version: 0.1.0
 platform: ruby
 authors:
 - Christian Zmasek
@@ -10,75 +9,137 @@ authors:
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2012-05-18 00:00:00.000000000 Z
+date: 2015-08-06 00:00:00.000000000 Z
 dependencies:
+- !ruby/object:Gem::Dependency
+  name: bio-logger
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.0'
 - !ruby/object:Gem::Dependency
   name: shoulda
-  requirement: &76510780 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.5.0
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: '0'
+        version: '3.5'
   type: :development
   prerelease: false
-  version_requirements: *76510780
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 3.5.0
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.5'
 - !ruby/object:Gem::Dependency
   name: rdoc
-  requirement: &76510420 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - "~>"
       - !ruby/object:Gem::Version
         version: '3.12'
   type: :development
   prerelease: false
-  version_requirements: *76510420
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.12'
 - !ruby/object:Gem::Dependency
   name: jeweler
-  requirement: &76510040 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.8.3
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
   type: :development
   prerelease: false
-  version_requirements: *76510040
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.8.3
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.8'
 - !ruby/object:Gem::Dependency
   name: bundler
-  requirement: &76509650 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.6.2
+    - - "~>"
       - !ruby/object:Gem::Version
-        version: 1.0.21
+        version: '1.6'
   type: :development
   prerelease: false
-  version_requirements: *76509650
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.6.2
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
 - !ruby/object:Gem::Dependency
   name: bio
-  requirement: &76524960 !ruby/object:Gem::Requirement
-    none: false
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ! '>='
+    - - ">="
       - !ruby/object:Gem::Version
         version: 1.4.2
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
   type: :development
   prerelease: false
-  version_requirements: *76524960
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 1.4.2
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.4'
 - !ruby/object:Gem::Dependency
-  name: rdoc
-  requirement: &76524250 !ruby/object:Gem::Requirement
-    none: false
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
     requirements:
-    - - ~>
+    - - ">="
       - !ruby/object:Gem::Version
-        version: '3.12'
+        version: 4.7.5
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.7'
   type: :development
   prerelease: false
-  version_requirements: *76524250
-description: Enables parsing of HMMER version 3 reports
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: 4.7.5
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '4.7'
+description: Enables programmatic parsing of HMMER version 3 reports
 email: gmail.com after donttrustben
 executables: []
 extensions: []
@@ -86,48 +147,51 @@ extra_rdoc_files:
 - LICENSE.txt
 - README.md
 files:
-- .document
-- .travis.yml
+- ".document"
+- ".travis.yml"
 - Gemfile
 - LICENSE.txt
 - README.md
 - Rakefile
 - VERSION
 - lib/bio-hmmer3_report.rb
-- lib/bio/appl/hmmer/hmmer3/report.rb
+- lib/bio/appl/hmmer/hmmer3/default_report.rb
+- lib/bio/appl/hmmer/hmmer3/tabular_report.rb
+- test/data/HMMER/hmmer3_onlyWholeSequenceNotDomains.txt
+- test/data/HMMER/hmmer3multidomainHit.txt
+- test/data/HMMER/hmmer3multidomainHitSimple.txt
 - test/data/HMMER/hmmscan_domtblout.out
 - test/data/HMMER/hmmscan_tblout.out
 - test/data/HMMER/hmmsearch_domtblout.out
 - test/data/HMMER/hmmsearch_domtblout_empty.out
 - test/data/HMMER/hmmsearch_tblout.out
+- test/data/HMMER/test637000001.hmmsearch.txt
 - test/helper.rb
+- test/unit/bio/appl/hmmer/test_hmmer3_default_report.rb
+- test/unit/bio/appl/hmmer/test_hmmer3_report_formatting.rb
 - test/unit/bio/appl/hmmer/test_hmmer3report.rb
 homepage: http://github.com/wwood/bioruby-hmmer3_report
 licenses:
 - MIT
+metadata: {}
 post_install_message: 
 rdoc_options: []
 require_paths:
 - lib
 required_ruby_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
-      segments:
-      - 0
-      hash: -284128881
 required_rubygems_version: !ruby/object:Gem::Requirement
-  none: false
   requirements:
-  - - ! '>='
+  - - ">="
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 1.8.17
+rubygems_version: 2.2.2
 signing_key: 
-specification_version: 3
+specification_version: 4
 summary: Enables parsing of HMMER version 3 reports
 test_files: []