This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Writing a bash loop to convert sams to bams

Hey all, I'm trying to write a small bash loop to iterate over all sam files in a directory converting them to bam. What I have so far is:

files=$(ls)
for f in "$files"
    do samtools view -S -b $f>"$f".bam
    done

But what I get when I run that is:

convert_sam_to_bam.sh: line 9: ACGGTC.1.sam
AGACCA.1.sam
AGCTTT.1.sam
AGGAAT.1.sam
[list of all sams in the directory]
TGACAT.1.sam
TTAGGC.1.sam
TTGACT.1.sam
TTGTCA.1.sam.bam: File name too long

I'm sure the problem is that I'm messing up with the quotations somewhere, but I can't for the life of me figure out where. Any thoughts? Thanks a lot in advanc!

alignment
• 3,915 views • link
updated by st.ph.n st.ph.n • written by raf.marcondes • raf.marcondes

This is a pure shell question. For starters, you don't need files=$(ls); for f in $files, you can simply do for f in * (or better, for f in *.sam). In fact, I think doing that will solve your problem as your current approach treats a set of filenames as a string instead of treating it as an array.

• 0 views • link
written by Ram Ram

1 answer 

for file in *.sam; do
    samtools view -S -b $file > "`basename $file .sam`.bam"
done
• 0 views • link
written by st.ph.n st.ph.n

You don't need the basename sub-shell call, you can simply use ${file/%sam/bam}. Bash has powerful parameter expansion.

• 0 views • link
written by Ram Ram

Log in to answer this question.

More posts like this