parse_fasta 1.9.2 → 2.0.0
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- checksums.yaml +8 -8
- data/.gitignore +1 -0
- data/.rspec +2 -0
- data/CHANGELOG.md +178 -0
- data/README.md +42 -215
- data/Rakefile +2 -4
- data/bin/console +14 -0
- data/bin/setup +8 -0
- data/lib/parse_fasta/error.rb +39 -0
- data/lib/parse_fasta/record.rb +88 -0
- data/lib/parse_fasta/seq_file.rb +221 -114
- data/lib/parse_fasta/version.rb +2 -2
- data/lib/parse_fasta.rb +5 -20
- data/spec/parse_fasta/record_spec.rb +115 -0
- data/spec/parse_fasta/seq_file_spec.rb +238 -0
- data/spec/parse_fasta_spec.rb +25 -0
- data/spec/spec_helper.rb +2 -44
- data/spec/test_files/cr.fa +1 -0
- data/spec/test_files/cr.fa.gz +0 -0
- data/spec/test_files/cr.fq +3 -0
- data/spec/test_files/cr.fq.gz +0 -0
- data/spec/test_files/cr_nl.fa +4 -0
- data/spec/test_files/cr_nl.fa.gz +0 -0
- data/spec/test_files/cr_nl.fq +8 -0
- data/spec/test_files/cr_nl.fq.gz +0 -0
- data/spec/test_files/multi_blob.fa.gz +0 -0
- data/spec/test_files/multi_blob.fq.gz +0 -0
- data/spec/test_files/not_a_seq_file.txt +1 -0
- data/{test_files/bad.fa → spec/test_files/poorly_catted.fa} +0 -0
- data/{test_files/test.fa → spec/test_files/seqs.fa} +0 -0
- data/spec/test_files/seqs.fa.gz +0 -0
- data/spec/test_files/seqs.fq +8 -0
- data/spec/test_files/seqs.fq.gz +0 -0
- metadata +49 -24
- data/lib/parse_fasta/fasta_file.rb +0 -232
- data/lib/parse_fasta/fastq_file.rb +0 -160
- data/lib/parse_fasta/quality.rb +0 -54
- data/lib/parse_fasta/sequence.rb +0 -174
- data/spec/lib/fasta_file_spec.rb +0 -212
- data/spec/lib/fastq_file_spec.rb +0 -143
- data/spec/lib/quality_spec.rb +0 -51
- data/spec/lib/seq_file_spec.rb +0 -357
- data/spec/lib/sequence_spec.rb +0 -188
- data/test_files/benchmark.rb +0 -99
- data/test_files/bogus.txt +0 -2
- data/test_files/test.fa.gz +0 -0
- data/test_files/test.fq +0 -8
- data/test_files/test.fq.gz +0 -0
checksums.yaml
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metadata.gz: !binary |-
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data.tar.gz: !binary |-
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SHA512:
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metadata.gz: !binary |-
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data/.gitignore
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data/.rspec
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data/CHANGELOG.md
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## Versions ##
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### 2.0.0 ###
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A weird feature of `Zlib::GzipReader` made it so that if a gzipped file was created like this.
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```bash
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gzip -c a.fa > z.fa.gz
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gzip -c b.fa >> z.fa.gz
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```
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Then the gzip reader would only read the lines from `a.fa` without some fiddling around. Since this was a pretty low level thing, I just decided to make a bunch of under the hood changes that I've been meaning to get to.
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#### Other things
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- Everything is namespaced under `ParseFasta` module
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- Removed `FastaFile` and `FastqFile` classes, `SeqFile` only remains
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- Removed `Sequence` and `Quality` classes. These might get put back in at some point, but I almost never used them anyway
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- `SeqFile#each_record` yields a `Record` object so you can use the same code to parse fastA and fastQ files
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- Other stuff that I'm forgetting!
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### 1.9.2 ###
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Speed up fastA `each_record` and `each_record_fast`.
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### 1.9.1 ###
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Speed up fastQ `each_record` and `each_record_fast`. Courtesy of
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[Matthew Ralston](https://github.com/MatthewRalston).
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### 1.9.0 ###
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Added "fast" versions of `each_record` methods
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(`each_record_fast`). Basically, they return sequences and quality
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strings as Ruby `Sring` objects instead of aa `Sequence` or `Quality`
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objects. Also, if the sequence or quality string has spaces, they will
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be retained. If this is a problem, use the original `each_record`
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methods.
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### 1.8.2 ###
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Speed up `FastqFile#each_record`.
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### 1.8.1 ###
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An error will be raised if a fasta file has a `>` in the
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sequence. Sometimes files are not terminated with a newline
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character. If this is the case, then catting two fasta files will
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smush the first header of the second file right in with the last
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sequence of the first file. This is bad, raise an error! ;)
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Example
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>seq1
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ACTG>seq2
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ACTG
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>seq3
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ACTG
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This will raise `ParseFasta::SequenceFormatError`.
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Also, headers with lots of `>` within are fine now.
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### 1.8 ###
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Add `Sequence#rev_comp`. It can handle IUPAC characters. Since
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`parse_fasta` doesn't check whether the seq is AA or NA, if called on
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an amino acid string, things will get weird as it will complement the
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IUPAC characters in the AA string and leave others.
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### 1.7.2 ###
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Strip spaces (not all whitespace) from `Sequence` and `Quality` strings.
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Some alignment fastas have spaces for easier reading. Strip these
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out. For consistency, also strips spaces from `Quality` strings. If
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there are spaces that don't match in the quality and sequence in a
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fastQ file, then things will get messed up in the FastQ file. FastQ
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shouldn't have spaces though.
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### 1.7 ###
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Add `SeqFile#to_hash`, `FastaFile#to_hash` and `FastqFile#to_hash`.
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### 1.6.2 ###
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`FastaFile::open` now raises a `ParseFasta::DataFormatError` when passed files
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that don't begin with a `>`.
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### 1.6.1 ###
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Better internal handling of empty sequences -- instead of raising
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errors, pass empty sequences.
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### 1.6 ###
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Added `SeqFile` class, which accepts either fastA or fastQ files. It
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uses FastaFile and FastqFile internally. You can use this class if you
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want your scripts to accept either fastA or fastQ files.
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If you need the description and quality string, you should use
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FastqFile instead.
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### 1.5 ###
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Now accepts gzipped files. Huzzah!
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### 1.4 ###
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Added methods:
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Sequence.base_counts
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Sequence.base_frequencies
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### 1.3 ###
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Add additional functionality to `each_record` method.
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#### Info ####
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I often like to use the fasta format for other things like so
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>fruits
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pineapple
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pear
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peach
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>veggies
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peppers
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parsnip
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peas
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rather than having this in a two column file like this
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fruit,pineapple
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fruit,pear
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fruit,peach
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veggie,peppers
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veggie,parsnip
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veggie,peas
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So I added functionality to `each_record` to keep each line a record
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separate in an array. Here's an example using the above file.
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info = []
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FastaFile.open(f, 'r').each_record(1) do |header, lines|
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info << [header, lines]
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end
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Then info will contain the following arrays
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['fruits', ['pineapple', 'pear', 'peach']],
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['veggies', ['peppers', 'parsnip', 'peas']]
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### 1.2 ###
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Added `mean_qual` method to the `Quality` class.
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### 1.1.2 ###
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Dropped Ruby requirement to 1.9.3
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(Note, if you want to build the docs with yard and you're using
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Ruby 1.9.3, you may have to install the redcarpet gem.)
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### 1.1 ###
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Added: Fastq and Quality classes
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### 1.0 ###
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Added: Fasta and Sequence classes
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Removed: File monkey patch
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### 0.0.5 ###
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Last version with File monkey patch.
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data/README.md
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#
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# ParseFasta #
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[![Gem Version](https://badge.fury.io/rb/parse_fasta.svg)](http://badge.fury.io/rb/parse_fasta) [![Build Status](https://travis-ci.org/mooreryan/parse_fasta.svg?branch=master)](https://travis-ci.org/mooreryan/parse_fasta) [![Coverage Status](https://coveralls.io/repos/mooreryan/parse_fasta/badge.svg)](https://coveralls.io/r/mooreryan/parse_fasta)
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Add this line to your application's Gemfile:
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```ruby
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gem 'parse_fasta'
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```
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And then execute:
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## Overview ##
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Provides nice, programmatic access to fasta and fastq files
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as providing Sequence and Quality helper classes. It's more
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lightweight than BioRuby. And more fun! ;)
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Provides nice, programmatic access to fasta and fastq files. It's faster and more lightweight than BioRuby. And more fun!
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## Documentation ##
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## Usage ##
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### 1.9.1 ###
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Speed up fastQ `each_record` and `each_record_fast`. Courtesy of
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[Matthew Ralston](https://github.com/MatthewRalston).
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### 1.9.0 ###
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Added "fast" versions of `each_record` methods
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(`each_record_fast`). Basically, they return sequences and quality
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strings as Ruby `Sring` objects instead of aa `Sequence` or `Quality`
|
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objects. Also, if the sequence or quality string has spaces, they will
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be retained. If this is a problem, use the original `each_record`
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methods.
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### 1.8.2 ###
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Speed up `FastqFile#each_record`.
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### 1.8.1 ###
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An error will be raised if a fasta file has a `>` in the
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sequence. Sometimes files are not terminated with a newline
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character. If this is the case, then catting two fasta files will
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smush the first header of the second file right in with the last
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sequence of the first file. This is bad, raise an error! ;)
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Example
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>seq1
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ACTG>seq2
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ACTG
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>seq3
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ACTG
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This will raise `ParseFasta::SequenceFormatError`.
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Also, headers with lots of `>` within are fine now.
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-
|
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### 1.8 ###
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-
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Add `Sequence#rev_comp`. It can handle IUPAC characters. Since
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`parse_fasta` doesn't check whether the seq is AA or NA, if called on
|
115
|
-
an amino acid string, things will get weird as it will complement the
|
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IUPAC characters in the AA string and leave others.
|
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-
|
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-
### 1.7.2 ###
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-
|
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Strip spaces (not all whitespace) from `Sequence` and `Quality` strings.
|
121
|
-
|
122
|
-
Some alignment fastas have spaces for easier reading. Strip these
|
123
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-
out. For consistency, also strips spaces from `Quality` strings. If
|
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there are spaces that don't match in the quality and sequence in a
|
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fastQ file, then things will get messed up in the FastQ file. FastQ
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shouldn't have spaces though.
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### 1.7 ###
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Add `SeqFile#to_hash`, `FastaFile#to_hash` and `FastqFile#to_hash`.
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### 1.6.2 ###
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`FastaFile::open` now raises a `ParseFasta::DataFormatError` when passed files
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that don't begin with a `>`.
|
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-
|
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### 1.6.1 ###
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-
|
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Better internal handling of empty sequences -- instead of raising
|
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|
-
errors, pass empty sequences.
|
141
|
-
|
142
|
-
### 1.6 ###
|
143
|
-
|
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|
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Added `SeqFile` class, which accepts either fastA or fastQ files. It
|
145
|
-
uses FastaFile and FastqFile internally. You can use this class if you
|
146
|
-
want your scripts to accept either fastA or fastQ files.
|
147
|
-
|
148
|
-
If you need the description and quality string, you should use
|
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|
-
FastqFile instead.
|
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|
-
|
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|
-
### 1.5 ###
|
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|
-
|
153
|
-
Now accepts gzipped files. Huzzah!
|
154
|
-
|
155
|
-
### 1.4 ###
|
156
|
-
|
157
|
-
Added methods:
|
158
|
-
|
159
|
-
Sequence.base_counts
|
160
|
-
Sequence.base_frequencies
|
161
|
-
|
162
|
-
### 1.3 ###
|
163
|
-
|
164
|
-
Add additional functionality to `each_record` method.
|
165
|
-
|
166
|
-
#### Info ####
|
167
|
-
|
168
|
-
I often like to use the fasta format for other things like so
|
169
|
-
|
170
|
-
>fruits
|
171
|
-
pineapple
|
172
|
-
pear
|
173
|
-
peach
|
174
|
-
>veggies
|
175
|
-
peppers
|
176
|
-
parsnip
|
177
|
-
peas
|
178
|
-
|
179
|
-
rather than having this in a two column file like this
|
180
|
-
|
181
|
-
fruit,pineapple
|
182
|
-
fruit,pear
|
183
|
-
fruit,peach
|
184
|
-
veggie,peppers
|
185
|
-
veggie,parsnip
|
186
|
-
veggie,peas
|
187
|
-
|
188
|
-
So I added functionality to `each_record` to keep each line a record
|
189
|
-
separate in an array. Here's an example using the above file.
|
190
|
-
|
191
|
-
info = []
|
192
|
-
FastaFile.open(f, 'r').each_record(1) do |header, lines|
|
193
|
-
info << [header, lines]
|
194
|
-
end
|
195
|
-
|
196
|
-
Then info will contain the following arrays
|
197
|
-
|
198
|
-
['fruits', ['pineapple', 'pear', 'peach']],
|
199
|
-
['veggies', ['peppers', 'parsnip', 'peas']]
|
200
|
-
|
201
|
-
### 1.2 ###
|
202
|
-
|
203
|
-
Added `mean_qual` method to the `Quality` class.
|
204
|
-
|
205
|
-
### 1.1.2 ###
|
206
|
-
|
207
|
-
Dropped Ruby requirement to 1.9.3
|
208
|
-
|
209
|
-
(Note, if you want to build the docs with yard and you're using
|
210
|
-
Ruby 1.9.3, you may have to install the redcarpet gem.)
|
211
|
-
|
212
|
-
### 1.1 ###
|
213
|
-
|
214
|
-
Added: Fastq and Quality classes
|
215
|
-
|
216
|
-
### 1.0 ###
|
217
|
-
|
218
|
-
Added: Fasta and Sequence classes
|
219
|
-
|
220
|
-
Removed: File monkey patch
|
221
|
-
|
222
|
-
### 0.0.5 ###
|
223
|
-
|
224
|
-
Last version with File monkey patch.
|
225
|
-
|
226
|
-
## Benchmark ##
|
227
|
-
|
228
|
-
Some quick and dirty benchmarks against `BioRuby`.
|
229
|
-
|
230
|
-
### FastaFile#each_record ###
|
231
|
-
|
232
|
-
You can see the test script in `benchmark.rb`.
|
233
|
-
|
234
|
-
user system total real
|
235
|
-
parse_fasta 1.920000 0.160000 2.080000 ( 2.145932)
|
236
|
-
parse_fasta fast 1.210000 0.160000 1.370000 ( 1.377770)
|
237
|
-
bioruby 4.330000 0.290000 4.620000 ( 4.655567)
|
238
|
-
|
239
|
-
Hot dog! It's faster :)
|
240
|
-
|
241
|
-
## Notes ##
|
242
|
-
|
243
|
-
Only the `SeqFile` class actually checks to make sure that you passed
|
244
|
-
in a "proper" fastA or fastQ file, so watch out.
|
35
|
+
Here are some examples of using ParseFasta. Don't forget to `require "parse_fasta"` at the top of your program!
|
36
|
+
|
37
|
+
Print header and length of each record.
|
38
|
+
|
39
|
+
```ruby
|
40
|
+
ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec|
|
41
|
+
puts [rec.header, rec.seq.length].join "\t"
|
42
|
+
end
|
43
|
+
```
|
44
|
+
|
45
|
+
You can parse fastQ files in exatcly the same way.
|
46
|
+
|
47
|
+
```ruby
|
48
|
+
ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec|
|
49
|
+
printf "Header: %s, Sequence: %s, Description: %s, Quality: %s\n",
|
50
|
+
rec.header,
|
51
|
+
rec.seq,
|
52
|
+
rec.desc,
|
53
|
+
rec.qual
|
54
|
+
end
|
55
|
+
```
|
56
|
+
|
57
|
+
The `Record#desc` and `Record#qual` will be `nil` if the file you are parsing is a fastA file.
|
58
|
+
|
59
|
+
```ruby
|
60
|
+
ParseFasta::SeqFile.open(ARGV[0]).each_record do |rec|
|
61
|
+
if rec.qual
|
62
|
+
puts "@#{rec.header}"
|
63
|
+
puts rec.seq
|
64
|
+
puts "+#{rec.desc}"
|
65
|
+
puts rec.qual
|
66
|
+
else
|
67
|
+
puts ">#{rec.header}"
|
68
|
+
puts rec.sequence
|
69
|
+
end
|
70
|
+
end
|
71
|
+
```
|
data/Rakefile
CHANGED
data/bin/console
ADDED
@@ -0,0 +1,14 @@
|
|
1
|
+
#!/usr/bin/env ruby
|
2
|
+
|
3
|
+
require "bundler/setup"
|
4
|
+
require "parse_fasta"
|
5
|
+
|
6
|
+
# You can add fixtures and/or initialization code here to make experimenting
|
7
|
+
# with your gem easier. You can also use a different console, if you like.
|
8
|
+
|
9
|
+
# (If you use this, don't forget to add pry to your Gemfile!)
|
10
|
+
# require "pry"
|
11
|
+
# Pry.start
|
12
|
+
|
13
|
+
require "irb"
|
14
|
+
IRB.start
|
data/bin/setup
ADDED
@@ -0,0 +1,39 @@
|
|
1
|
+
# Copyright 2014 - 2016 Ryan Moore
|
2
|
+
# Contact: moorer@udel.edu
|
3
|
+
#
|
4
|
+
# This file is part of parse_fasta.
|
5
|
+
#
|
6
|
+
# parse_fasta is free software: you can redistribute it and/or modify
|
7
|
+
# it under the terms of the GNU General Public License as published by
|
8
|
+
# the Free Software Foundation, either version 3 of the License, or
|
9
|
+
# (at your option) any later version.
|
10
|
+
#
|
11
|
+
# parse_fasta is distributed in the hope that it will be useful,
|
12
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
13
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
14
|
+
# GNU General Public License for more details.
|
15
|
+
#
|
16
|
+
# You should have received a copy of the GNU General Public License
|
17
|
+
# along with parse_fasta. If not, see <http://www.gnu.org/licenses/>.
|
18
|
+
|
19
|
+
module ParseFasta
|
20
|
+
# Contains the Error classes that ParseFasta API will raise
|
21
|
+
module Error
|
22
|
+
|
23
|
+
# All ParseFasta errors inherit from ParseFastaError
|
24
|
+
class ParseFastaError < StandardError
|
25
|
+
end
|
26
|
+
|
27
|
+
# Raised when the input file doesn't look like fastA or fastQ
|
28
|
+
class DataFormatError < ParseFastaError
|
29
|
+
end
|
30
|
+
|
31
|
+
# Raised when the file is not found
|
32
|
+
class FileNotFoundError < ParseFastaError
|
33
|
+
end
|
34
|
+
|
35
|
+
# Raised when fastA sequences have a '>' in them
|
36
|
+
class SequenceFormatError < ParseFastaError
|
37
|
+
end
|
38
|
+
end
|
39
|
+
end
|
@@ -0,0 +1,88 @@
|
|
1
|
+
# Copyright 2014 - 2016 Ryan Moore
|
2
|
+
# Contact: moorer@udel.edu
|
3
|
+
#
|
4
|
+
# This file is part of parse_fasta.
|
5
|
+
#
|
6
|
+
# parse_fasta is free software: you can redistribute it and/or modify
|
7
|
+
# it under the terms of the GNU General Public License as published by
|
8
|
+
# the Free Software Foundation, either version 3 of the License, or
|
9
|
+
# (at your option) any later version.
|
10
|
+
#
|
11
|
+
# parse_fasta is distributed in the hope that it will be useful,
|
12
|
+
# but WITHOUT ANY WARRANTY; without even the implied warranty of
|
13
|
+
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
|
14
|
+
# GNU General Public License for more details.
|
15
|
+
#
|
16
|
+
# You should have received a copy of the GNU General Public License
|
17
|
+
# along with parse_fasta. If not, see <http://www.gnu.org/licenses/>.
|
18
|
+
|
19
|
+
module ParseFasta
|
20
|
+
class Record
|
21
|
+
|
22
|
+
# @!attribute header
|
23
|
+
# @return [String] the full header of the record without the '>'
|
24
|
+
# or '@'
|
25
|
+
# @!attribute seq
|
26
|
+
# @return [String] the sequence of the record
|
27
|
+
# @!attribute desc
|
28
|
+
# @return [String or Nil] if the record is from a fastA file, it
|
29
|
+
# is nil; else, the description line of the fastQ record
|
30
|
+
# @!attribute qual
|
31
|
+
# @return [String or Nil] if the record is from a fastA file, it
|
32
|
+
# is nil; else, the quality string of the fastQ record
|
33
|
+
attr_accessor :header, :seq, :desc, :qual
|
34
|
+
|
35
|
+
# The constructor takes keyword args.
|
36
|
+
#
|
37
|
+
# @example Init a new Record object for a fastA record
|
38
|
+
# Record.new header: "apple", seq: "actg"
|
39
|
+
# @example Init a new Record object for a fastQ record
|
40
|
+
# Record.new header: "apple", seq: "actd", desc: "", qual: "IIII"
|
41
|
+
#
|
42
|
+
# @param header [String] the header of the record
|
43
|
+
# @param seq [String] the sequence of the record
|
44
|
+
# @param desc [String] the description line of a fastQ record
|
45
|
+
# @param qual [String] the quality string of a fastQ record
|
46
|
+
#
|
47
|
+
# @raise [SequenceFormatError] if a fastA sequence has a '>'
|
48
|
+
# character in it
|
49
|
+
def initialize args = {}
|
50
|
+
@header = args.fetch :header
|
51
|
+
|
52
|
+
@desc = args.fetch :desc, nil
|
53
|
+
@qual = args.fetch :qual, nil
|
54
|
+
|
55
|
+
@qual.gsub!(/\s+/, "") if @qual
|
56
|
+
|
57
|
+
seq = args.fetch(:seq).gsub(/\s+/, "")
|
58
|
+
|
59
|
+
if @qual # is fastQ
|
60
|
+
@seq = seq
|
61
|
+
else # is fastA
|
62
|
+
@seq = check_fasta_seq(seq)
|
63
|
+
end
|
64
|
+
end
|
65
|
+
|
66
|
+
# Compare attrs of this rec with another
|
67
|
+
#
|
68
|
+
# @param rec [Record] a Record object to compare with
|
69
|
+
#
|
70
|
+
# @return [Bool] true or false
|
71
|
+
def == rec
|
72
|
+
self.header == rec.header && self.seq == rec.seq &&
|
73
|
+
self.desc == rec.desc && self.qual == rec.qual
|
74
|
+
end
|
75
|
+
|
76
|
+
private
|
77
|
+
|
78
|
+
def check_fasta_seq seq
|
79
|
+
if seq.match ">"
|
80
|
+
raise ParseFasta::Error::SequenceFormatError,
|
81
|
+
"A sequence contained a '>' character " +
|
82
|
+
"(the fastA file record separator)"
|
83
|
+
else
|
84
|
+
seq
|
85
|
+
end
|
86
|
+
end
|
87
|
+
end
|
88
|
+
end
|