Removing text after a delimiter up to a certain point in Bash/Linux

Question

target_id       tpm     tpm     tpm     tpm     tpm     tpm     tpm     tpm     tpm     tpm     tpm
PB.1.1|1:6643-11779(-)|transcript/55100 9207.33 13266.4 15244.3 2844.27 2708.52 2731.91 3193.83 2675.78 3413.74 4001.   37      3332.62
PB.2.1|1:11961-16372(+)|transcript/24543        14.2016 27.8457 29.6335 7.14533 7.34512 7.64953 8.71118 6.87958 7.228   98      6.3592  5.94422
PB.2.2|1:11961-16373(+)|transcript/30117        2.70221 2.74091 2.81943 3.99669 2.69497 2.82466 3.01701 2.62054 2.958   49      2.48024 2.44429
PB.2.3|1:11962-16374(+)|transcript/35082        1.21596 1.76974 2.24733 1.76356 2.05692 1.7765  1.65524 1.44116 1.970   26      2.16288 1.50391
PB.3.1|1:27833-34327(+)|transcript/44399        71.0007 131.61  145.062 24.9771 23.0295 24.9615 26.8033 20.4961 25.36   6       26.6337 21.9282
PB.4.1|1:39316-44582(-)|transcript/24897        26.5017 37.3793 43.4624 11.1199 8.80527 8.18072 12.612  10.0202 12.24   37      8.06654 7.04677
PB.4.2|1:39317-44595(-)|transcript/39771        9.23018 9.89149 7.58203 10.1779 8.67577 7.9611  8.5775  9.83895 7.638   42      6.40913 6.58653
PB.4.3|1:39318-43423(-)|transcript/29985        20.8149 20.6359 14.5622 3.89209 3.92182 3.4396  4.53606 2.6505  3.979   53      2.92956 2.63565
PB.5.1|1:44841-49854(-)|transcript/24019        36.302  19.7211 18.3107 71.1272 70.6337 65.391  62.6371 61.8226 67.62   43      55.2076 57.7828

So I want to remove after the first | up to the first decimal numbers. For example I want this outputted:

PB.1.1| 9207.33 13266.4 15244.3 2844.27 2708.52 2731.91 3193.83 2675.78 3413.74 4001.   37      3332.62.

I've tried using the cut command but have only been able to cut everything after the first delimiter, any pointers?

Answer 1

A simple solution would be to use awk and specify | as your field separator.

awk 'BEGIN {FS="|"} ; {print $1"|"$3}'

This would print the first and third fields. So for your example I get:

PB.1.1|transcript/55100 9207.33 13266.4 15244.3 2844.27 2708.52 2731.91 3193.83 2675.78 3413.74 4001.   37      3332.62
PB.2.1|transcript/24543        14.2016 27.8457 29.6335 7.14533 7.34512 7.64953 8.71118 6.87958 7.228   98      6.3592  5.94422
PB.2.2|transcript/30117        2.70221 2.74091 2.81943 3.99669 2.69497 2.82466 3.01701 2.62054 2.958   49      2.48024 2.44429
PB.2.3|transcript/35082        1.21596 1.76974 2.24733 1.76356 2.05692 1.7765  1.65524 1.44116 1.970   26      2.16288 1.50391
PB.3.1|transcript/44399        71.0007 131.61  145.062 24.9771 23.0295 24.9615 26.8033 20.4961 25.36   6       26.6337 21.9282
PB.4.1|transcript/24897        26.5017 37.3793 43.4624 11.1199 8.80527 8.18072 12.612  10.0202 12.24   37      8.06654 7.04677
PB.4.2|transcript/39771        9.23018 9.89149 7.58203 10.1779 8.67577 7.9611  8.5775  9.83895 7.638   42      6.40913 6.58653
PB.4.3|transcript/29985        20.8149 20.6359 14.5622 3.89209 3.92182 3.4396  4.53606 2.6505  3.979   53      2.92956 2.63565
PB.5.1|transcript/24019        36.302  19.7211 18.3107 71.1272 70.6337 65.391  62.6371 61.8226 67.62   43      55.2076 57.7828

Answer 2

sed -e 's/|.\{33\}//w test2.txt' test.txt This worked alright, thanks everyone regardless.

Answer 3

Tested with Below command and worked fine

command

sed 's/|.*|transcript\/[0-9]\{5\} /| /g'  filename