meta file table
Hi,
How can I generate a meta file table from a list of text files?
I have a text file with multiple file names, like so:
ID1_GENDER_TREATMENT.fastq
ID2_GENDER_TREATMENT.fastq
.
.
.
IDn_GENDER_TREATMENT.fastq
I would like to generate a table that looks like this:
ID GENDER TREATMENT
ID1 gender treatment
ID2 gender treatment
.
. .
I am new in bioinformatics and I am not sure how to do this.
Thanks!
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ATpoint
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figueroacg •
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figueroacg •
1 answer
Assume you had files like this:
$ ls *.fastq
ID1_GENDER1_TREATMENT1.fastq ID2_GENDER2_TREATMENT2.fastq ID3_GENDER3_TREATMENT3.fastq
Then do:
$ ls *.fastq | awk -F "_" 'OFS="\t" {if(NR==1)print "ID", "GENDER", "TREATMENT"} {gsub(".fastq","");print $1, $2, $3}'
ID GENDER TREATMENT
ID1 GENDER1 TREATMENT1
ID2 GENDER2 TREATMENT2
ID3 GENDER3 TREATMENT3
OFS="\t" will make it a tab-delimited list. Change that if you want alternative delimiters.
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