README.rdoc in bio-gff3-0.8.3 vs README.rdoc in bio-gff3-0.8.4

@@ -56,5 +56,93 @@
 == Copyright
 
 Copyright (C) 2010,2011 Pjotr Prins <[e-mail]> 
 
 
+
+  Fetch and assemble GFF3 types (e.g. ORF, mRNA, CDS) + print in FASTA format. 
+
+    gff3-fetch [--low-mem] [--validate] type [filename.fa] filename.gff3
+
+  Where (NYI == Not Yet Implemented):
+
+    --translate     : output as amino acid sequence 
+    --validate      : validate GFF3 file by translating
+    --fix           : check 3-frame translation and fix, if possible 
+    --fix-wormbase  : fix 3-frame translation on ORFs named 'gene1'
+    --no-assemble   : output each record as a sequence -- NYI
+    --add-phase     : output records using phase (useful w. no-assemble CDS to AA) --NYI
+  
+  type is any valid type in the GFF3 definition. For example:
+
+    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
+
+  and the following performance options:
+
+    --cache full    : load all in RAM (fast)
+    --cache none    : do not load anything in memory (slow)
+    --low-mem       : use LRU cache (limit RAM use, fast) -- NYI
+    --max-cpus num  : use num threads -- NYI
+    --emboss        : use EMBOSS translation (fast) -- NYI
+
+  Multiple GFF3 files can be used. With external FASTA files, always the last
+  one before the GFF3 filename is matched.
+
+  Note that above switches are only partially implemented at this stage. Full
+  feature support is projected Feb. 2011.
+
+  Examples:
+
+    Assemble mRNA and CDS information from test.gff3 (which includes sequence information)
+
+      gff3-fetch mRNA test/data/gff/test.gff3
+      gff3-fetch CDS test/data/gff/test.gff3
+
+    Find CDS records from external FASTA file, adding phase and translate to protein sequence
+
+      gff3-fetch --no-assemble --add-phase --translate CDS test/data/gff/MhA1_Contig1133.fa test/data/gff/MhA1_Contig1133.gff3
+
+    Find mRNA from external FASTA file, without loading everything in RAM
+
+      gff3-fetch --cache none mRNA test/data/gff/test-ext-fasta.fa test/data/gff/test-ext-fasta.gff3   
+      gff3-fetch --cache none mRNA test/data/gff/test-ext-fasta.fa test/data/gff/test-ext-fasta.gff3   
+
+    Validate GFF3 file using EMBOSS translation and validation
+
+      gff3-fetch --cache none --validate --emboss mRNA test/data/gff/test-ext-fasta.fa test/data/gff/test-ext-fasta.gff3   
+
+    Find GENEID predicted terminal exons
+
+      gff3-fetch terminal chromosome1.fa geneid.gff3
+
+== Performance
+
+time gff3-fetch cds m_hapla.WS217.dna.fa m_hapla.WS217.gff3 > test.fa
+
+  Cache      real     user     sys
+  ----------------------------------------------------
+  full       12m41s   12m28s   0m09s (0.8.0 Jan. 2011)
+  none      504m39s  477m49s  26m50s (0.8.0 Jan. 2011)
+  ----------------------------------------------------
+
+where
+
+   52M m_hapla.WS217.dna.fa
+  456M m_hapla.WS217.gff3
+
+ruby 1.9.2p136 (2010-12-25 revision 30365) [x86_64-linux]
+on an 8 CPU, 2.6 GHz (6MB cache), 16 GB RAM machine. 
+
+== Cite
+
+  If you use this software, please cite 
+  
+    http://dx.doi.org/10.1093/bioinformatics/btq475
+
+== Copyright
+
+Copyright (C) 2010,2011 Pjotr Prins <[e-mail]> 
+