CODEWITHSUNDEEP
linuxsortingcatfastq
user2883746
user2883746

Reputation: 21

Concatenate Files In Order Linux Command

I just started learning to use command line. Hopefully this is not a dump question.

I have the following files in my directory:

L001_R1_001.fastq 
L002_R2_001.fastq 
L004_R1_001.fastq 
L005_R2_001.fastq
L001_R2_001.fastq 
L003_R1_001.fastq 
L004_R2_001.fastq 
L006_R1_001.fastq
L002_R1_001.fastq 
L003_R2_001.fastq 
L005_R1_001.fastq 
L006_R2_001.fastq

You can see in the filenames, it's a mix of R1 and R2 and the numbers after L00 are not sorted.

I want to concatenate files in the order of filename, separately for R1 and R2 files.

If I do it manually, it will look like the following:

# for R1 files
cat L001_R1_001.fastq L002_R1_001.fastq L003_R1_001.fastq L004_R1_001.fastq L005_R1_001.fastq L006_R1_001.fastq > R1.fastq


# for R2 files
cat L001_R2_001.fastq L002_R2_001.fastq L003_R2_001.fastq L004_R2_001.fastq L005_R2_001.fastq L006_R2_001.fastq > R2.fastq

Could you please help me write a script that I can re-use later? Thank you!

Upvotes: 2

Views: 8351

Answers (2)

pts
pts

Reputation: 87271

cat `ls -- *_R1_*.fastq | sort` >R1.fastq
cat `ls -- *_R2_*.fastq | sort` >R2.fastq

The | sort is not needed on most systems because ls sorts the files by name.

If the names of the files contain whitespace, then do this first:

IFS='
'

Upvotes: 4

jkshah
jkshah

Reputation: 11703

Try using wildcard character *. It will automatically expand file names in alphabetical order. 

cat L*_R1_001.fastq > R1.fastq
cat L*_R2_001.fastq > R2.fastq

EDIT:

If above command doesn't give desired sorting, try overriding locale setting using LC_ALL=C as sugested by Fredrik Pihl 

LC_ALL=C cat L*_R1_001.fastq > R1.fastq

Upvotes: 1

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