for loop is not working within my script

StackOverflow https://stackoverflow.com/questions/15539481

문제

I made a script in bash that run blastx.

#!/bin/sh -l 
# $Id: Barrine.sh federicogaiti $

echo "Right now it is:"
date
echo ""
function usage() {
echo "Barrine.sh script by Federico Gaiti, March 2013."
echo ""
echo "Run Blastx"
echo ""
echo "Usage: "
echo "Barrine.sh <All contigs (fasta extension)> <Number of fasta split sequences> <Head file with PBS command where you set up account, walltime, etc..> "
echo ""
echo "Example: "
echo "Barrine.sh InputFasta n Head "
echo ""
exit 1
}

# Testing if the number of arguments is correct
if [ $# != 3 ]
then
    usage
        exit
    fi

### Declaring variables
InputFasta=$1    MY ORIGINAL FASTA FILE WITH ALL THE SEQUENCES
n=$2                 NUMBER OF FILES I WANT MY FASTA FILE SPLIT
Head=$3           PBS OPTIONS
n4=$((n/4))
n41=$((n/4 + 1))
n2=$((n/2))
n21=$((n/2 + 1))
n43=$((n/4 * 3))
n431=$((n/4*3 + 1))


echo Loading Modules
module load ucsc_utilities/20130122
wait


echo Split input FASTA in n FASTA file
faSplit sequence ${InputFasta} ${n} ${InputFasta}_Split_S 
wait



echo blastx command splitting it in 4 jobs to make it faster
    for i in {000..0$n4} ; do echo "blastx -query ${InputFasta}_Split_S$i.fa -evalue 0.0001 -max_target_seqs 100 -db nr -num_threads 8 -outfmt '7 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore score' -out ${InputFasta}_blastx$i.csv" ; done > ${InputFasta}_Job1.sh


    for i in {0$n41..$n2} ; do echo "blastx -query ${InputFasta}_Split_S$i.fa -evalue 0.0001 -max_target_seqs 100 -db nr -num_threads 8 -outfmt '7 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore score' -out ${InputFasta}_blastx$i.csv" ; done > ${InputFasta}_Job2.sh


    for i in {$n21..$n43} ; do echo "blastx -query ${InputFasta}_Split_S$i.fa -evalue 0.0001 -max_target_seqs 100 -db nr -num_threads 8 -outfmt '7 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore score' -out ${InputFasta}_blastx$i.csv" ; done > ${InputFasta}_Job3.sh


    for i in {$n431..$n} ; do echo "blastx -query ${InputFasta}_Split_S$i.fa -evalue 0.0001 -max_target_seqs 100 -db nr -num_threads 8 -outfmt '7 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore score' -out ${InputFasta}_blastx$i.csv" ; done > ${InputFasta}_Job4.sh

wait


echo Head the PBS commands to the Job files 
    for i in {1..4} 
        do 
        cat ${Head} ${InputFasta}_Job$i.sh | sed "s/BlastJob/BlastJob_$i/g" > ${InputFasta}_BlastJob$i.sh 
        done

I will then submit the 4 Jobs to barrine server. What I am supposed to obtain is 4 jobs containing this:

    blastx -query TEST_Split_S000.fa -evalue 0.0001 -max_target_seqs 100 -db nr -num_threads 8 -outfmt '7 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore score' -out TEST_blastx000.csv
blastx -query TEST_Split_S001.fa -evalue 0.0001 -max_target_seqs 100 -db nr -num_threads 8 -outfmt '7 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore score' -out TEST_blastx001.csv
blastx -query TEST_Split_S002.fa -evalue 0.0001 -max_target_seqs 100 -db nr -num_threads 8 -outfmt '7 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore score' -out TEST_blastx002.csv
blastx -query TEST_Split_S003.fa -evalue 0.0001 -max_target_seqs 100 -db nr -num_threads 8 -outfmt '7 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore score' -out TEST_blastx003.csv
blastx -query TEST_Split_S004.fa -evalue 0.0001 -max_target_seqs 100 -db nr -num_threads 8 -outfmt '7 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore score' -out TEST_blastx004.csv
blastx -query TEST_Split_S005.fa -evalue 0.0001 -max_target_seqs 100 -db nr -num_threads 8 -outfmt '7 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore score' -out TEST_blastx005.csv
blastx -query TEST_Split_S006.fa -evalue 0.0001 -max_target_seqs 100 -db nr -num_threads 8 -outfmt '7 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore score' -out TEST_blastx006.csv
blastx -query TEST_Split_S007.fa -evalue 0.0001 -max_target_seqs 100 -db nr -num_threads 8 -outfmt '7 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore score' -out TEST_blastx007.csv
............
blastx -query TEST_Split_S050.fa -evalue 0.0001 -max_target_seqs 100 -db nr -num_threads 8 -outfmt '7 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore score' -out TEST_blastx050.csv

But what I got in my script is just:

blastx -query TEST_Split_S{000..050}.fa -evalue 0.0001 -max_target_seqs 100 -db nr -num_threads 8 -outfmt '7 qseqid qlen sseqid pident length mismatch gapopen qstart qend sstart send ppos evalue bitscore score' -out TEST_blastx{000..050}.csv

Someone can help me in solving the problem? If I use the for loop outside my script works fine.

Thanks for help

도움이 되었습니까?

해결책

Brace expansion happens early.

Parameter expansion happens later, so you can't use variables or other parameters in a way that controls brace expansion.

From the bash(1) man page:

The order of expansions is: brace expansion, tilde expansion, parameter, variable and arithmetic expansion and command substitution (done in a left-to-right fashion), word splitting, and pathname expansion.

This will prevent statements like for i in {000..0$n4} ; do from working as intended.

Also, be sure to remember the -v and -x arguments to display the actual commands executed.

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