bio-cigar¶ ↑
Parser for the cigar sequence alignment format.
Note: this software is under active development!
Installation¶ ↑
gem install bio-cigar
Usage¶ ↑
require 'bio-cigar' # An example from http://davetang.org/wiki/tiki-index.php?page=SAM # CIGAR: 3S8M1D6M4S cigar_string = '3S8M1D6M4S' cigar = Bio::Cigar.new(cigar_string) #=> Bio::Cigar object # REF: TCGCCCGTCTAGCATACGC # READ: gggGTGTAACC-GACTAGgggg # MATCH:---001000000010010---- ref = 'TCGCCCGTCTAGCATACGCCCGTCTAGCATACGC' query = 'gggGTGTAACCGACTAGgggg' answer = cigar.percent_identity(ref, query) answer.should == [ 20.0, #20% Identity 3, #3 matches 12 #12 mismatches ]
It can also be used directly on SAM format alignments (Bio::DB::Alignment
objects), which are produced by bio-samtools
:
sam = Bio::DB::Alignment.new sam.cigar = '196M54S' sam.pos = 1150 sam.seq = 'ACTGCCGGTGTTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGCCCAGGGCTACACACGTGCTACAATGGCCGTTACAAAGCGTCGCTAACCCGCGAGGGGGAGCCAATCGCAAAAAAGCGGCCTCAGTTCAGATTGCAGTCTGCAACTCGACTGCATGAAGTTGGAATCCCTAGTAATCGCGTGTCATTAGCGCGCGGTGAATACGTCCCTGCTCCTTGCACTCACCGCCCGT' ref = 'GAGCGAACGTTAGCGGCGGGCTTAACACATGCAAGTCGAACGAGAATGAAGGAGCAATCCTTCTAGTAAAGTGGCGGACGGGTGCGTAACACGTGGATAATCTACCTTCCGGCGGGGGACAACAGTTCGAAAGGACTGCTAATACCGCGTACGTCGGCGAGAGCTCAGGCTCTTGTCGGGAAAGATGGCCAATCCTTGGAAGCTGTCACCGGAAGATGAATCCGCGGCCCATCAGGTAGTTGGTGAGGTAATGGCTCACCAAGCCTAAGACGGGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGCGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGGCAATGGGCGAAAGCCTGACCCAGCCACGCCGCGTGAGTGATGAAGGCCTTCGGGTCGTAAAGCTCTGTGGGGAGGGACGAACAAGTGCGTATCGAATAAATACGTGCCCTGACGGTACCTCCTTAGCAAGCACCGGCTAACCATGTGCCAGCAGCCGCGGTAATACATGGGGTGCAAACGTTGCTCGGAATTATTGGGCGTAAAGCGCGCGTAGGCGGTCGCTTAAGTCGGATGTGAAATCCCTCGGCTTAACTGAGGAAGTGCATCCGAGACTGAATGGCTAGAGTACGAAAGAGGGTCGNNNNNTTCCCGGTGTAGAGGTGAAATTCGTAGATATCGGGAGGAACACCGGCGGCGAAGGCGGCGACCTGGTTCGAGACTGACGCTGAGGCGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGGATGCTAGATGTTTCTGGTATTGACCCCGGAGGCGTCGTAGCTAACGCGATAAGCATCCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTCAATTTGACGCAACGCGAAGAACCTTACCTGGGTTGGAACCCTCCAGAAGTCCGCAGAGATGTGGATGTGCTCGCAAGAGAACTGGATGTCCAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCGTTAGTTGCTAACAGTTCGGCTGAGCACTCTAACGAGACTGCCGGTGTTAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTATGCCCAGGGCTACACACGTGCTACAATGGTCGTTACAAAGCGTCGCTAACCCGCGAGGGGGAGCTAATCGCAAAAAAGCGGCCTCAGTTCAGATTGCAGTCTGCAACTCGACTGCATGAAGTTGGAATCGCTAGTAATCCCTGATCAGCAGGCAGGGGTGAATACGTTCCCGGGCC' sam.percent_identity(ref).should == [ 98.46938775510205, 193, 3 ]
The API doc is online. For more code examples see the test files in the source tree.
Project home page¶ ↑
Information on the source tree, documentation, examples, issues and how to contribute, see
github.com/wwood/bioruby-cigar
The BioRuby community is on IRC server: irc.freenode.org, channel: bioruby.
Cite¶ ↑
This software is currently unpublished.
Biogems.info¶ ↑
This Biogem is published at (biogems.info/index.html#bio-cigar)
Copyright¶ ↑
Copyright © 2013 Ben J Woodcroft. See LICENSE.txt for further details.