README.md in parse_fasta-1.5.2 vs README.md in parse_fasta-1.6.0
- old
+ new
@@ -1,8 +1,8 @@
# parse_fasta #
-[](http://badge.fury.io/rb/parse_fasta)
+[](http://badge.fury.io/rb/parse_fasta) [](https://travis-ci.org/mooreryan/parse_fasta) [](https://coveralls.io/r/mooreryan/parse_fasta)
So you want to parse a fasta file...
## Installation ##
@@ -18,60 +18,73 @@
$ gem install parse_fasta
## Overview ##
-I wanted a simple, fast way to parse fasta and fastq files so I
-wouldn't have to keep writing annoying boilerplate parsing code
-everytime I go to do something with a fasta or fastq file. I will
-probably add more, but likely only tasks that I find myself doing over
-and over.
+Provides nice, programmatic access to fasta and fastq files, as well
+as providing Sequence and Quality helper classes. It's more
+lightweight than BioRuby. And more fun! ;)
## Documentation ##
Checkout
-[parse_fasta docs](http://rubydoc.info/gems/parse_fasta/1.5.0/frames)
-to see the full documentation.
+[parse_fasta docs](http://rubydoc.info/gems/parse_fasta/1.6.0/frames)
+for the full api documentation.
## Usage ##
Some examples...
A little script to print header and length of each record.
require 'parse_fasta'
- FastaFile.open(ARGV.first, 'r').each_record do |header, sequence|
+ FastaFile.open(ARGV[0]).each_record do |header, sequence|
puts [header, sequence.length].join("\t")
end
And here, a script to calculate GC content:
- FastaFile.open(ARGV.first, 'r').each_record do |header, sequence|
+ FastaFile.open(ARGV[0]).each_record do |header, sequence|
puts [header, sequence.gc].join("\t")
end
Now we can parse fastq files as well!
- FastqFile.open(ARGV.first, 'r').each_record do |head, seq, desc, qual|
- puts [header, seq, desc, qual.qual_scores.join(',')].join("\t")
+ FastqFile.open(ARGV[0]).each_record do |head, seq, desc, qual|
+ puts [header, qual.qual_scores.join(',')].join("\t")
end
+What if you don't care if the input is a fastA or a fastQ? No problem!
+
+ SeqFile.open(ARGV[0]).each_record do |head, seq|
+ puts [header, seq].join "\t"
+ end
+
## Versions ##
-### 1.5.0 ###
+### 1.6 ###
+Added `SeqFile` class, which accepts either fastA or fastQ files. It
+uses FastaFile and FastqFile internally. You can use this class if you
+want your scripts to accept either fastA or fastQ files.
+
+If you need the description and quality string, you should use
+FastqFile instead.
+
+### 1.5 ###
+
Now accepts gzipped files. Huzzah!
-### 1.4.0 ###
+### 1.4 ###
Added methods:
Sequence.base_counts
Sequence.base_frequencies
-### 1.3.0 ###
+### 1.3 ###
Add additional functionality to `each_record` method.
#### Info ####
@@ -106,26 +119,26 @@
Then info will contain the following arrays
['fruits', ['pineapple', 'pear', 'peach']],
['veggies', ['peppers', 'parsnip', 'peas']]
-### 1.2.0 ###
+### 1.2 ###
Added `mean_qual` method to the `Quality` class.
### 1.1.2 ###
Dropped Ruby requirement to 1.9.3
(Note, if you want to build the docs with yard and you're using
Ruby 1.9.3, you may have to install the redcarpet gem.)
-### 1.1.0 ###
+### 1.1 ###
Added: Fastq and Quality classes
-### 1.0.0 ###
+### 1.0 ###
Added: Fasta and Sequence classes
Removed: File monkey patch
@@ -133,30 +146,30 @@
Last version with File monkey patch.
## Benchmark ##
-Take these with a grain of salt since `BioRuby` is a big module
-module with lots of features and error checking, whereas `parse_fasta`
-is meant to be lightweight and easy to use for my own research.
+Perhaps this isn't exactly fair since `BioRuby` is a big module with
+lots of features and error checking, whereas `parse_fasta` is meant to
+be lightweight and easy to use for my own research. Oh well ;)
### FastaFile#each_record ###
-Just for fun, I wanted to compare the execution time to that of
-BioRuby. I calculated sequence 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're probably wondering...How does it compare to BioRuby in some
+super accurate benchmarking tests? Lucky for you, I calculated
+sequence 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`.
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 64.530000 1.740000 66.270000 ( 67.081502)
bioruby 116.250000 2.260000 118.510000 (120.223710)
-I just wanted a nice, clean way to parse fasta files, but being nearly
-twice as fasta as BioRuby doesn't hurt either!
+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.
@@ -165,18 +178,15 @@
this_fastq 62.610000 1.660000 64.270000 ( 64.389408)
bioruby_fastq 165.500000 2.100000 167.600000 (167.969636)
### Sequence#gc ###
-I played around with a few different implementations for the `#gc`
-method and found this one to be the fastest.
-
-The test is done on random strings mating `/[AaCcTtGgUu]/`. `this_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 scale, the test 1 string was 2,000,000 bases,
+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)
@@ -187,9 +197,23 @@
this_gc 3 0.120000 0.000000 0.120000 ( 0.185434)
bioruby_gc 3 8.060000 0.020000 8.080000 ( 8.659071)
Nice!
+Troll: "But Ryan, when will you find the GC of an 8,000,000 base
+sequence?"
+
+Me: "Step off, troll!"
+
+## Test suite & docs ##
+
+For a good time, you could clone this repo and run the test suite with
+rspec! Or if you just don't trust that it works like it should. The
+specs probably need a little clean up...so fork it and clean it up ;)
+
+Same with the docs. Clone the repo and build them yourself with `yard`
+if you are in need of some excitement.
+
## Notes ##
-Currently in doesn't check whether your file is actually a fasta file
-or anything, so watch out.
+Only the `SeqFile` class actually checks to make sure that you passed
+in a "proper" fastA or fastQ file, so watch out.