Synopsis

ExactMatches checks whether a given read or its reverse complement matches a not-so-long reference sequence or not.

Motivation

This code was generated to look for rRNA exact matching contaminations from tophat2 accepted reads.

Code Example

Usage:

ExactMatches <reads.fa> <ref_seq.fa> nentriesref output_prefix

where:

• reads.fa: fasta file with accepted reads. Example:

  HWI-ST933:227:C8C7YACXX:1:2215:17204:32048 GCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGACAGGAGAATGGCGTGAACCCCGGGGGGCGGA HWI-ST933:227:C8C7YACXX:1:2113:14665:43703 CCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTACAGGGCCCCACCACCACGC HWI-ST933:227:C8C7YACXX:1:2309:5571:96349 CTTGTCTCTACTAAAAAAATACAAAAAAATTAGCTGGGCGTGGTGGTGGGGCCCTGTAGTCCCAGCTAC HWI-ST933:227:C8C7YACXX:1:2216:15383:28082 GAAGTGCGTGCCTGTAGTCCCAACTGCTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAAGTA HWI-ST933:227:C8C7YACXX:1:2106:16798:18157 CGTCTCTACTAAAAAAAAATACAAAATTAACTGGGTGTGGTGGCACACGCCTGTAATCCCAGCTACTCG

• ref_seq.fa: fasta file with the reference sequence(s) (more than one allowed).

  gi|555853|gb|U13369.1|HSU13369 Human ribosomal DNA complete repeating unit GCTGACACGCTGTCCTCTGGCGACCTGTCGTCGGAGAGGTTGGGCCTCCGGATGCGCGCGGGGCTCTGGC CTCACGGTGACCGGCTAGCCGGCCGCGCTCCTGCCTTGAGCCGCCTGCCGCGGCCCGCGGGCCTGCTGTT CTCTCGCGCGTCCGAGCGTCCCGACTCCCGGTGCCGGCCCGGGTCCGGGTCTCTGACCCACCCGGGGGCG GCGGGGAAGGCGGCGAGGGCCACCGTGCCCCGTGCGCTCTCCGCTGCGGGCGCCCGGGGCGCCGCACAAC CCCACCCGCTGGCTCCGTGCCGTGCGTGTCAGGCGTTCTCGTCTCCGCGGGGTTGTCCGCCGCCCCTTCC CCGGAGTGGGGGGTGGCCGGAGCCGATCGGCTCGCTGGCCGGCCGGCCTCCGCTCCCGGGGGGCTCTTCG ATCGATGTGGTGACGTCGTGCTCTCCCGGGCCGGGTCCGAGCCGCGACGGGCGAGGGGCGGACGTTCGTG GCGAACGGGACCGTCCTTCTCGCTCCGCCCGCGCGGTCCCCTCGTCTGCTCCTCTCCCCGCCCGCCGGCC GGCGTGTGGGAAGGCGTGGGGTGCGGACCCCGGCCCGACCTCGCCGTCCCGCCCGCCGCCTTCGCTTCGC

• nentriesref: number of reference sequences contained in ref_seq.fa

Output

The output is written into two files:

• output_prefix+"exactmatch.fa": contains reads (or their reverse complementary) that match exactly the reference entry [i]. In case it is the reverse complementary that matches, it is the one to be outputted.

• output_prefix+"noexactmatch.fa": contains reads that do not match exactly the reference entry [i], neither do their reverse complementary counterparts.

Installation

1. Download the package.
2. The Makefile was written for a g++ compiler. Customize the compiler and compiling flags.
3. Run make.
4. Executable should land in the folder bin, and should be called ExactMatches.

Structure of the package.

Package contents:

 |- bin/      
     |- ExactMatches    
 |- include/    
     |- FastaFile.h   
     |- Sequence.h  
     |- utils.h  
 |- obj/ (object files land here. Not included in repository)  
 |- src/  
     |- ExactMatches.cc  (main)   
     |- FastaFile.cc  
     |- Sequence.cc  
     |- utils.cc   (general functions)  
 |- test_files/  
     |- reads.fa  
     |- ref_seq.fa   
     |- test_output_exactmatch.fa   
     |- test_output_noexactmatch.fa   

Tests

In folder test_files there are two test input files:

• reads.fa : example of a file with reads.
• ref_seq.fa : example of a fasta reference file.

and two output files: test_output_exactmatch.fa, test_output_noexactmatch.fa

The test file refs_seq.fa contains two entries, so, one can run the executable by doing:

bin/ExactMatches test_files/reads.fa test_files/ref_seq.fa 2 test_output