CODEWITHSUNDEEP
bash
zoe
zoe

Reputation: 311

Concatenate files with same partial id BASH

I have a directory with many fq.gz files. I want to loop over the filenames and concatenate any files with the same partial ID. For example out of the 1000 files in the directory, these six need to be concatenated into a single file (as they share the same ID From "L1" onwards)

141016-FC012-L1-N707-S504--123V_pre--Hs--R1.fq.gz
141031-FC01229-L1-N707-S504--123V_pre--Hs--R1.fq.gz
141020-FC01209-L1-N707-S504--123V_pre--Hs--R1.fq.gz
141027-FC013-L1-N707-S504--123V_pre--Hs--R1.fq.gz
141023-FC01219-L1-N707-S504--123V_pre--Hs--R1.fq.gz

Can anyone help??

Upvotes: 0

Views: 72

Answers (1)

PesaThe
PesaThe

Reputation: 7519

Probably not the best way, but this might do what you need:

while IFS= read -r -d '' id; do
    cat *"$id" > "/some/location/${id%.fq.gz}_grouped.fq.gz"
done < <(printf '%s\0' *.fq.gz | cut -zd- -f3- | sort -uz)

This will create files with the following format:

<ID>_grouped.fq.gz
L1-N707-S504--123V_pre--Hs--R1_grouped.fq.gz
...
...

Upvotes: 1

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