CODEWITHSUNDEEP
bash
The Nightman
The Nightman

Reputation: 5759

Use zcat to batch combine a list of files

I have a folder with a number of files in it which need to be combined and i'm looking for a good command to do it with. The files look like this:

Concatenate Together:
A1_S1_L001_R1_001.fastq.gz
A1_S1_L002_R1_001.fastq.gz
A1_S1_L003_R1_001.fastq.gz
A1_S1_L004_R1_001.fastq.gz

Concatenate Together:
A1_S1_L001_R2_001.fastq.gz
A1_S1_L002_R2_001.fastq.gz
A1_S1_L003_R2_001.fastq.gz
A1_S1_L004_R2_001.fastq.gz

Concatenate Together:
B1_S1_L001_R1_001.fastq.gz
B1_S1_L002_R1_001.fastq.gz
B1_S1_L003_R1_001.fastq.gz
B1_S1_L004_R1_001.fastq.gz

Concatenate Together:
B1_S1_L001_R2_001.fastq.gz
B1_S1_L002_R2_001.fastq.gz
B1_S1_L003_R2_001.fastq.gz
B1_S1_L004_R2_001.fastq.gz

etc.

So the pattern is that for hundreds of files the first letter and number (A1 or B1 here) refers to a group which contains in it two subgroups (R1 and R2). The main groups are A1-H1, A2-H2, and A3-H3. Within each subgroup there are four files (L001, L002, L003, L004).

Is there a good way to simply combine these with zcat (or really any other way)?

Upvotes: 0

Views: 189

Answers (1)

redneb
redneb

Reputation: 23850

Something like this should do it:

cd "/path/to/the/directory" || exit 1
for num in {1..3}; do
    for letter in {A..H}; do
        for subgroup in R1 R2; do
            zcat "$letter$num"_S1_L*_"$subgroup"_001.fastq.gz > "$letter$num-$subgroup"
        done
    done
done

You may have to adjust the name (and possibly path) of the output files. I used "$letter$num-$subgroup" so e.g. B1-R1.

Upvotes: 2

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