lancelothk

#!/bin/bash
if [ ! -d "$3" ]; then
	mkdir $3
fi
for file in $2/*
do
	outputFile=${file/$2/$3}
	#echo "perl $1/fastq2fasta_out.pl $file ${outputFile/fastq/fasta}"
	perl $1/fastq2fasta_out.pl $file ${outputFile}.fasta
done

lancelothk

copy from http://www.ibm.com/developerworks/aix/library/au-unixtext/
Example of shell script – change file extension:
$ cat setup_files.ksh
mkdir /tmp/mv_demo
[ ! -d /tmp/mv_demo ] && exit

cd /tmp/mv_demo
mkdir tmp JPG 'pictures 1'
touch a.JPG b.jpg c.Jpg d.jPg M.jpG P.jpg JPG_file.JPG JPG.file2.jPg file1.JPG.Jpg 'tmp/
pic 2.Jpg' 10.JPG.bak 'pictures 1/photo.JPG' JPG/readme.txt JPG/sos.JPG

lancelothk

copy from http://www.ibm.com/developerworks/aix/library/au-unixtext/
Example of shell script – string extraction:
$ cat string_example1.sh
#!/bin/sh
FILEPATH=/home/w/wyoes/samples/ksh_samples-v1.0.ksh
echo '${FILEPATH}      =' ${FILEPATH}      "  # the full filepath"
echo '${#FILEPATH}     =' ${#FILEPATH}      "  # length of the string"
echo '${FILEPATH%.*}   =' ${FILEPATH%.*}   "  # truncate right of the last dot"
echo '${FILEPATH%%.*}  =' ${FILEPATH%%.*}  "  # truncate right of the first dot"
echo '${FILEPATH%%/w*} =' ${FILEPATH%%/w*} "  # truncate right of the first /w"

lancelothk

copy from http://sed.sourceforge.net/sed1line.txt
-------------------------------------------------------------------------
USEFUL ONE-LINE SCRIPTS FOR SED (Unix stream editor)        Dec. 29, 2005
Compiled by Eric Pement - pemente[at]northpark[dot]edu        version 5.5

Latest version of this file (in English) is usually at:
   http://sed.sourceforge.net/sed1line.txt
   http://www.pement.org/sed/sed1line.txt

This file will also available in other languages: