#!/bin/csh

# Run faToNib on a folder of *.fa sequences

# First argument: directory with genome sequences in fasta format

set genomeDir = $1

# First argument: extension for fasta chromosome files (ex: fa) 

set ext = $2

# Go to directory holding GoldenPath files, one per chromosome
cd $genomeDir

# Do for each chr file (ex: chr1.fsa)
foreach chrFile (*.${ext})

# Make new name by replacing .fa with .nib 
# and place in /cluster/db0/blat directory
echo "Creating nib file (${genomeDir}/`basename $chrFile .${ext}`.nib) from $chrFile"

# Run faToNib
/cluster/lsfpool/bin/faToNib -softmask $chrFile $genomeDir/`basename $chrFile .${ext}`.nib

end