batch_convert_faidx.sh

#! /usr/bin
# put the coordinates in a bed file

infile=$1
while read chr start end 
do
samtools faidx ref.fasta $chr:$start-$end >> test.fa
done <$infile

coordinates2seq.py

# Use the cruzdb python package https://github.com/brentp/cruzdb
from cruzdb import sequence 
print sequence.sequence(‘hg19’,’chr1’, 100000, 100010)
# cactaagcaca
# 1 based!

coordinates2sequences.sh

# download twoBitToFa here http://hgdownload.cse.ucsc.edu/admin/exe/  
twoBitToFa http://hgdownload.cse.ucsc.edu/gbdb/hg19/hg19.2bit test.fa -seq=chr1 -start=100000 -end=100010
cat test.fa
>chr1:100000-100010
actaagcaca
# Note that it is 0 based cooridnates system

# Use betools get fasta http://bedtools.readthedocs.org/en/latest/content/tools/getfasta.html
# you need a fasta file of the whole genome, and a bed file containing the cooridnates 
bedtools getfasta -fi UCSC_hg19_genome.fa -bed input.bed -fo out.fa
cat out.fa
>chr1:100000-100010
actaagcaca
# it is also 0 based 

# Use samtools faidx
# First, index your fasta file (only have to do this once) 
samtools faidx reference.fa  
# then extract the sequences you want 
samtools faidx ref.fasta chr1:100000-100010
>chr1:100000-100010
cactaagcaca
# note that it is 1 based !