extract_fasta

extract_fasta is a very easy tool for fasta file(s) extraction from another fasta file.Run this tool within this directory by bash

Dependencies

1. samtools dependency samtools should be installed in /usr/local/bin/samtools

otherwise you have to edit the path in the perl_script2.pl

Usage

sh extract_fasta.sh -q query_id.txt -f sequence.fasta 

make sure that your sequence.fasta file is

>fasta_01
AATGCTATGTGACATATGACTCCTTCGAACAGATTCTGGTTTATCAGACTTATAACTCCT
GGTACTTAGTATTGCGTGACTAGATACAAGCAAGTATCAAAACTACAATCAACTGTTAAC

and your query id is "fasta_01"

This tool can not read the fasta file that have

>fasta_01|genename
AATGCTATGTGACATATGACTCCTTCGAACAGATTCTGGTTTATCAGACTTATAACTCCT
GGTACTTAGTATTGCGTGACTAGATACAAGCAAGTATCAAAACTACAATCAACTGTTAAC

and your query id is "fasta_01"

although it is a nice tool to make your job easy

we will improve it.