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fasta_parser's Introduction

fasta_parser

Basic package used to parse a file in the Fasta format

It provides basic functionality such as:

  • Quick sequence retrieval
  • Get number of sequences in the file
  • Print out the sequence ids

In the future, I plan to add new features to this package

Installation

'cd' to the directory containing the package's source and type:

make

You will see the differenct executable files in the ./bin directory

Usage

getseq

Before using getseq with a Fasta file you need to index it by doing:

makeix <input.fa>

Then, you can use getseq to fetch a particular sequence:

getseq <input.fa> <seqid>

getids

Program to print out the ids in <input.fa>

getseqno

Program to print out the number of sequences in <input.fa>

fasta_parser's People

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