Renaming files in Shell Script Linux

Question

I want to rename files I have downloaded from the following script:

exec < input_list.txt
while read line
do
get $line
wget ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/$2/$4
# Rename $4
mv $4 $1"_"$3".bam"
done

The input file (input_list.txt) is tab delimited and contains four columns. The first, $1= name, $2= wget address, $3= factor and $4 is the file name.

A549    wgEncodeBroadHistone    H2azDex100nm    wgEncodeBroadHistoneA549H2azDex100nmAlnRep1.bam

I want to rename $4 (the file that has been downloaded) to a shorter file name that only includes the corresponding $1 and $3 terms. For example, wgEncodeBroadHistoneA549H2azDex100nmAlnRep1.bam becomes A549_H2azDex100nm.bam

I've played around with " but I keep getting error messages for the mv command and that $4 is a bad variable name. Any suggestions would be greatly appreciated.

I think it would help to see the actual field in 'input_list.txt'. $4, the variable, may not actually correspond to the name of the file that is downloaded from wget. — philshem
– philshem, Commented Aug 13, 2013 at 14:48

konsolebox · Accepted Answer · 2013-08-13 14:48:05Z

4

You don't need to rename the file if you use wget's -O option:

#!/bin/bash

[ -n "$BASH_VERSION" ] || {
    echo "You need Bash to run this script."
    exit 1
}

while IFS=$'\t' read -a INPUT; do
    wget -O "${INPUT[0]}_${INPUT[2]}.bam" "ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/${INPUT[1]}/${INPUT[3]}"
done < input_list.txt

Make sure you save the file in UNIX file format like script.sh and run bash script.sh.

answered Aug 13, 2013 at 14:48

konsolebox

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