Bash troubleshooting: Not a valid identifier

Question

Beginner here trying to get a pipeline working in bash. If somebody can see why when I run the following I get:

-bash: `$i': not a valid identifier,

that would be really helpful. Also if there are other mistakes please let me know

for $i in /home/regionstextfile; do tabix /sequences/human_variation/snps/genotypes.vcf.gz $i | vcftools --window-pi 10000 >> /home/Testgenomesdata/genomesregions.txt; done

The idea is for each line in regionstextfile (which contains genome coordinates) run a program called tabix in the vcf.bz file, then with the output run vcftools with the specified options, then put all the outputs into the genomesregions.txt file.

Do the lines contain whitespace (spaces or tabs)? – jedwards Jun 19 '12 at 07:41 — jedwards, Jun 19 '12 at 07:41

Igor Chubin · Accepted Answer · 2012-06-19T07:43:04.453

That must be so:

for i in `</home/regionstextfile`
do 
  tabix /sequences/human_variation/snps/genotypes.vcf.gz $i | vcftools --window-pi 10000 >> /home/Testgenomesdata/genomesregions.txt
done

When you use a variable (e.g. assign value to it or export it, or do anything but with the variable itself) you write its name without $; when you use a value of a variable you write $.

EDIT:

When region names contains spaces but each region is in a separate line, you need while:

cat /home/regionstextfile | while read i
do 
  tabix /sequences/human_variation/snps/genotypes.vcf.gz "$i" | vcftools --window-pi 10000 >> /home/Testgenomesdata/genomesregions.txt
done

As long as the lines in the textfile doesn't contain whitespace, this should work. — jedwards, Jun 19 '12 at 07:42

score 1 · Answer 2 · answered Jun 19 '12 at 09:49

The same thing without cat :

while read i
do
  tabix /sequences/human_variation/snps/genotypes.vcf.gz "$i" | vcftools --window-pi 10000 >> /home/Testgenomesdata/genomesregions.txt
done < /home/regionstextfile

Remark <file.txt could not work unless IFS=''

OLDIFS="$IFS"
IFS=''
for i in `</home/regionstextfile`
do
  tabix /sequences/human_variation/snps/genotypes.vcf.gz $i | vcftools --window-pi 10000 >> /home/Testgenomesdata/genomesregions.txt
done
IFS="$OLDIFS"

Bash troubleshooting: Not a valid identifier

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