README.md in parse_fasta-1.9.1 vs README.md in parse_fasta-1.9.2
- old
+ new
@@ -64,10 +64,14 @@
seqs = FastaFile.open(ARGV[0]).to_hash
## Versions ##
+### 1.9.2 ###
+
+Speed up fastA `each_record` and `each_record_fast`.
+
### 1.9.1 ###
Speed up fastQ `each_record` and `each_record_fast`. Courtesy of
[Matthew Ralston](https://github.com/MatthewRalston).
@@ -219,62 +223,21 @@
Last version with File monkey patch.
## Benchmark ##
-**NOTE**: These benchmarks are against an older version of
- `parse_fasta`.
-
Some quick and dirty benchmarks against `BioRuby`.
### FastaFile#each_record ###
-Calculating sequence length length for each fasta record with both the
-`each_record` method from this gem and using the `FastaFormat` class
-from BioRuby. You can see the test script in `benchmark.rb`.
+You can see the test script in `benchmark.rb`.
-The test file contained 2,009,897 illumina reads and the file size
-was 1.1 gigabytes. Here are the results from Ruby's `Benchmark` class:
+ user system total real
+ parse_fasta 1.920000 0.160000 2.080000 ( 2.145932)
+ parse_fasta fast 1.210000 0.160000 1.370000 ( 1.377770)
+ bioruby 4.330000 0.290000 4.620000 ( 4.655567)
- user system total real
- parse_fasta 64.530000 1.740000 66.270000 ( 67.081502)
- bioruby 116.250000 2.260000 118.510000 (120.223710)
-
Hot dog! It's faster :)
-
-### FastqFile#each_record ###
-
-The same sequence length test as above, but this time with a fastq
-file containing 4,000,000 illumina reads.
-
- user system total real
- this_fastq 62.610000 1.660000 64.270000 ( 64.389408)
- bioruby_fastq 165.500000 2.100000 167.600000 (167.969636)
-
-### Sequence#gc ###
-
-The test is done on random strings matcing `/[AaCcTtGgUu]/`. `this_gc`
-is `Sequence.new(str).gc`, and `bioruby_gc` is
-`Bio::Sequence::NA.new(str).gc_content`.
-
-To see how the methods scales, the test 1 string was 2,000,000 bases,
-test 2 was 4,000,000 and test 3 was 8,000,000 bases.
-
- user system total real
- this_gc 1 0.030000 0.000000 0.030000 ( 0.029145)
- bioruby_gc 1 2.030000 0.010000 2.040000 ( 2.157512)
-
- this_gc 2 0.060000 0.000000 0.060000 ( 0.059408)
- bioruby_gc 2 4.060000 0.020000 4.080000 ( 4.334159)
-
- this_gc 3 0.120000 0.000000 0.120000 ( 0.185434)
- bioruby_gc 3 8.060000 0.020000 8.080000 ( 8.659071)
-
-Nice!
-
-Troll: "When will you find the GC of an 8,000,000 base sequence?"
-
-Me: "Step off, troll!"
## Notes ##
Only the `SeqFile` class actually checks to make sure that you passed
in a "proper" fastA or fastQ file, so watch out.