Find loop with variable file and path naming

Question

I'm trying to do a bash loop to run a simple process over all files with extension .sam that can be found on a directory and its subdirectories, and use the same name (exc extension) for the output as its input, with output directed to the same folder in which the input was found.

I got to the following:

for file in $(find ~/data/finch_data/combruns_BF_genomes -name "*.sam" -type f); do 
    name="${file%.sam}"
    dir=$(pwd $file)
    samtools view -Sb "$dir"/"$name".sam > "$dir"/"$name".bam
done

but I'm getting this message:

...
>bash:/home/madzays/qsub//home/madzays/data/finch_data/combruns_ZF_transcriptomes/ZBND81X_gff/filteredfirstZBND81X_gff.bam: No such file or directory
>bash:/home/madzays/qsub//home/madzays/data/finch_data/combruns_ZF_transcriptomes/ZBND81X_gff/filteredsecZBND81X_gff.bam: No such file or directory
>bash:/home/madzays/qsub//home/madzays/data/finch_data/combruns_ZF_transcriptomes/ZBND82V_gff/filteredfirstZBND82V_gff.bam: No such file or directory
...

What could be wrong? thanks

Check the path, it includes /home/madzays/ twice, which should be incorrect. — Pedro Lobito
– Pedro Lobito, Commented Apr 8, 2018 at 1:22
dir=$(pwd) not dir=$(pwd $file), but it's not the issue here — kyodev
– kyodev, Commented Apr 8, 2018 at 1:45
I suggest: samtools view -Sb "$name.sam" > ... (without $dir) — kyodev
– kyodev, Commented Apr 8, 2018 at 1:47
Yeah this worked. But why? I thought find returned only the file name, but it returns the whole path, up to the file name! — Madza Farias-Virgens
– Madza Farias-Virgens, Commented Apr 8, 2018 at 20:44

LMC · Accepted Answer · 2018-04-08 01:14:01Z

1

Seems to me that namevariable does not contains what you want. Try getting name with basename instead

for file in $(find ~/data/finch_data/combruns_BF_genomes -name "*.sam" -type f); do name="$(basename $file .sam)" dir=$(pwd $file); samtools view -Sb "$dir"/"$name".sam > "$dir"/"$name".bam; done

answered Apr 8, 2018 at 1:14

LMC

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1 Comment

Madza Farias-Virgens Over a year ago

Yeah. The name variable already included the whole path, up to the file name.

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