Problem with sample names in the file created using awk

Question

I have some data like below:

dir1
  |___dir2
         |___dir3
               |____files
                      |____TGH4_1.tar.gz
                      |____TGH4_2.tar.gz
                      |____IOP5_1.tar.gz
                      |____IOP5_2.tar.gz
                      |____RGH2_btre_1.tar.gz
                      |____RGH2_btre_2.tar.gz
                      |____QWE6_btre_1.tar.gz
                      |____QWE6_btre_2.tar.gz

inside folder dir3 I created a script test.awk which has code like below:

BEGIN {
    FS="[/_]"; OFS="\t"
    print "sample", "Second", "Third"
}
NR%2 { second = $0; next }
{ print $2, second, $0 }

Using the test.awk I created a file:

printf '%s\n' $PWD/files/* | awk -f test.awk > test.txt

The output test.txt I got is like below:

sample  Second  Third
dir1    /dir1/dir2/dir3/H0032/files/TGH4_1.tar.gz   /dir1/dir2/dir3/H0032/files/TGH4_2.tar.gz
dir1    /dir1/dir2/dir3/H0032/files/IOP5_1.tar.gz   /dir1/dir2/dir3/H0032/files/IOP5_2.tar.gz
dir1    /dir1/dir2/dir3/H0032/files/RGH2_btre_1.tar.gz  /dir1/dir2/dir3/H0032/files/RGH2_btre_2.tar.gz
dir1    /dir1/dir2/dir3/H0032/files/QWE6_btre_1.tar.gz  /dir1/dir2/dir3/H0032/files/QWE6_btre_2.tar.gz

The output should look like below:

sample  Second  Third
TGH4    /dir1/dir2/dir3/H0032/files/TGH4_1.tar.gz   /dir1/dir2/dir3/H0032/files/TGH4_2.tar.gz
IOP5    /dir1/dir2/dir3/H0032/files/IOP5_1.tar.gz   /dir1/dir2/dir3/H0032/files/IOP5_2.tar.gz
RGH2_btre   /dir1/dir2/dir3/H0032/files/RGH2_btre_1.tar.gz  /dir1/dir2/dir3/H0032/files/RGH2_btre_2.tar.gz
QWE6_btre   /dir1/dir2/dir3/H0032/files/QWE6_btre_1.tar.gz  /dir1/dir2/dir3/H0032/files/QWE6_btre_2.tar.gz

Ed Morton · Accepted Answer · 2022-10-04 13:19:59Z

1

Change:

BEGIN { FS="[/_]" ... }
...
{ print $2, second, $0 }

to:

BEGIN { FS="/" ... }
...
{
    sample = $NF
    sub(/_[^_]*$/,"",sample)
    print sample, second, $0
}

Your code is printing dir1 because that's the 2nd field of /dir1/dir2/dir3/H0032/files/TGH4_2.tar.gz given your FS setting and your code says print $2....

answered Oct 4, 2022 at 13:19

Ed Morton

36k6 gold badges25 silver badges60 bronze badges

1

Thank you very much again Ed Morton !!

stack_learner
– stack_learner

2022-10-04 13:25:56 +00:00
Commented Oct 4, 2022 at 13:25

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