bin/gff3-fetch in bio-gff3-0.8.5 vs bin/gff3-fetch in bio-gff3-0.8.6

@@ -23,20 +23,20 @@
 
     mRNA             : assemble mRNA
     CDS              : assemble CDS 
     exon             : list all exons
     gene|ORF         : list gene ORFs 
-    other            : use any type from GFF3 definition, e.g. 'Terminate' -- NYI
+    other            : use any type from GFF3 definition, e.g. 'Terminate'
 
   and the following performance options:
 
 		--parser bioruby : use BioRuby GFF3 parser (slow)
-    --parser line    : use GFF3 line parser -- in preparation
-    --parser block   : use GFF3 block parser (optimistic) -- NYI
+    --parser line    : use GFF3 line parser (faster, default)
+    --block          : parse GFF3 by block (optimistic) -- NYI
     --cache full     : load all in RAM (fast, default)
     --cache none     : do not load anything in memory (slow)
-    --cache lru      : use LRU cache (limit RAM use, fast) -- NYI
+    --cache lru      : use least recently used cache (limit RAM use, fast) -- NYI
     --max-cpus num   : use num threads -- NYI
     --emboss         : use EMBOSS translation (fast) -- NYI
 
   Where (NYI == Not Yet Implemented):
 
@@ -72,26 +72,50 @@
 
     Fine tuning output - show errors only
 
       gff3-fetch mRNA test/data/gff/test.gff3 --trace ERROR
 
+    Fine tuning outpt - show messages matching regex 
+
+      gff3-fetch mRNA test/data/gff/test.gff3 --trace '=msg =~ /component/'
+
     Fine tuning output - write log messages to file.log
 
       gff3-fetch mRNA test/data/gff/test.gff3 --trace ERROR --logger file.log
 
+For more information on output, see the bioruby-logger plugin.
+
 == Performance
 
 time gff3-fetch cds m_hapla.WS217.dna.fa m_hapla.WS217.gff3 2> /dev/null > test.fa 
 
-  Cache              real     user     sys
+  Digesting parser:
+
+  Cache              real     user     sys  version     RAM
   ------------------------------------------------------------
   full,bioruby       12m41    12m28    0m09 (0.8.0)
   full,line          12m13    12m06    0m07 (0.8.5)
-  none,bioruby      504m39   477m49   26m50 (0.8.0)
-  lru,bioruby        ?
-  ----------------------------------------------------
+  full,line,lazy     11m51    11m43    0m07 (0.8.6)     6,600M
 
+  none,bioruby      504m     477m     26m50 (0.8.0)
+  none,line         297m     267m     28m36 (0.8.5)       
+  none,line,lazy    132m     106m     26m01 (0.8.6)       650M
+
+  lru,bioruby       533m     510m     22m47 (0.8.5)
+  lru,line          353m     326m     26m44 (0.8.5)  1K
+  lru,line          305m     281m     22m30 (0.8.5) 10K
+  lru,line,lazy     182m     161m     21m10 (0.8.6) 10K
+  lru,line,lazy      75m      75m      0m17 (0.8.6) 50K   730M
+  ------------------------------------------------------------
+
+  Block parser:
+
+  Cache              real     user     sys  gff3 version
+  ------------------------------------------------------------
+  in preparation
+  ------------------------------------------------------------
+
 where
 
    52M m_hapla.WS217.dna.fa
   456M m_hapla.WS217.gff3
 
@@ -130,43 +154,47 @@
 Bio::Log::CLI.trace('info')
 
 options = OpenStruct.new()
 
 # ---- Default options
-options.parser = :bioruby
+options.parser = :line
 
 opts = OptionParser.new() { |opts|
   opts.on_tail("-h", "--help", "Show help and examples") {
     print(opts)
     print USAGE
     exit()
   }
 
-  opts.on("--parser [bioruby,line]", String, "Parser (default bioruby)") do |p|
+  opts.on("--parser [bioruby,line]", String, "Parser (default line)") do |p|
     case p.downcase
       when 'bioruby'
         options.parser = :bioruby
       when 'line'
         options.parser = :line
       else
         raise 'Unknown --parser option'
     end
   end
 
-  opts.on("--cache [none,full]", String, "Caching (default full)") do |cache|
+  opts.on("--cache [full,lru,none]", String, "Caching (default full)") do |cache|
     case cache.downcase
       when 'none'
         options.cache = :cache_none
-      # when 'lru'
-      #   options.cache = :cache_lru
+      when 'lru'
+        options.cache = :cache_lru
       when 'full'
         options.cache = :cache_full
       else
         raise 'Unknown --cache option'
     end
   end
 
+  opts.on("--block", "Parse by block") do |b|
+    options.block = true
+  end
+
   opts.on("--no-assemble", "output sequences without assembling") do |b|
     options.no_assemble = true
   end
 
   opts.on("--phase", "adjust for phase (useful for CDS --no-assemble --translate)") do |b|
@@ -227,19 +255,24 @@
   end
 
   opts = {}
   opts[:validate]         = options.validate
   opts[:parser]           = options.parser
+  opts[:block]            = options.block
   opts[:cache_components] = options.cache
   opts[:cache_records]    = options.cache
   opts[:fasta_filename]   = fastafn if fastafn
   opts[:fix_wormbase]     = options.fix_wormbase
   opts[:fix]              = options.fix
   opts[:no_assemble]      = options.no_assemble
   opts[:phase]            = options.phase
   opts[:debug]            = options.debug
 
+  include Bio::GFFbrowser::Helpers::Logger
+  debug $:.to_s
+  debug opts.to_s
+  log_sys_info("BaseLine")
   gff3 = Bio::GFFbrowser::GFF3.new(fn,opts)
 
   gff = gff3.assembler
   writer = Bio::GFFbrowser::FastaWriter.new(options.translate, options.validate)
 
@@ -263,11 +296,14 @@
     when 'cds'
           gff.each_CDS_seq do | id, seq |
             writer.put(id,seq)
           end
     else
-      raise "Unknown action on type <#{gfftype}>"
+          gff.each_seq(gfftype.downcase) do | id, seq |
+            writer.put(id,seq)
+          end
   end
+  log_sys_info("Done")
   fastafn = nil
 end