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Asked: 2026-06-19T00:06:07+00:00

I’ve started using a linux machine and I’m trying to do simple things…but very

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I’ve started using a linux machine and I’m trying to do simple things…but very hard for me.
I need to select some specific lines that match with those reported in a second file.
Pratically I have a first file that is made like this:

>aba19  EN1 enl.or11    http://mar2043  annotation not avaliable
MASESEMGVVASJDHAGISFGVDDASDASDAFGDFGHWFACFQLIGIFLAYCLSRAITNN
QSDHKAJSDHKASJHKJAHKHKJSDGHYEIV
>clat38 EN2 enl.o   http://mar20s/Gene/Summary?5    annotation not avaliable
MNCEDCHILNAEAFKSKKDASDADICKSLKICGLVFGILALTLIVLFWGSKHFWPEVPKK
AYDMEHTFYSNGERGYCCASDSDDIYCSDRRGNRYCRRVCEPLLGYYPYPYCYQGGRVIC
RVIMPCDASDASDAOPWEIPQWFHNDJBVHAOISDOUIAODGNWWVARMLGRV
>coll9  EN4 ens4    http://mar2010.arch/Genary?g=E9 annotation not avaliable
MASKALDHLFKLJLÒFJASDJKLASDLAFJLFJFJLFJLAJFLKJFLAKFJFJLAFJLAL
ASDLASKDJASLKDJASLKJFALSKDJALKDJSKLDJLSDKJASLDKJSLDKSDLAKJKS
SILDUAISDALSDJALKDJASDLFATT 
>hihi9  EN9 ens44   http://mar2010.ariens/Geary?g=EN7   annotation not    avaliable
MGSLDLAÈPWOEMWBZMKSJDHAJKSDHAKSDHSDHSDHOASDAKSJDHKASJDHAAKHL
KTLSDKLHRFSDFHPHFGCJLJLJRKKFLDSFCGTVGEFAGGGDTHNNVCLSSVFVSEDG
HSDFSDWFKLGGMETVCSDFKVSQATPEFSSSDLFFDSRIQSIRDPASIPPEEMSPEFTT
LPECHGHARDAFSFGTLVESLLTILNEQVSADVLSSFQQTLHSTLLNPIPKCRPALCTLL
SDFLSDJFKLSDFLSKDFJM

And I have a second file with the list of patterns that I need to “extract” from the first file. The second file look like this:

>clat38
>coll9

Pratically I would like to have an output like this:

>clat38 EN2 enl.o   http://mar20s/Gene/Summary?5    annotation not avaliable
MNCEDCHILNAEAFKSKKDASDADICKSLKICGLVFGILALTLIVLFWGSKHFWPEVPKK
AYDMEHTFYSNGERGYCCASDSDDIYCSDRRGNRYCRRVCEPLLGYYPYPYCYQGGRVIC
RVIMPCDASDASDAOPWEIPQWFHNDJBVHAOISDOUIAODGNWWVARMLGRV
>coll9  EN4 ens4    http://mar2010.arch/Genary?g=E9 annotation not avaliable
MASKALDHLFKLJLÒFJASDJKLASDLAFJLFJFJLFJLAJFLKJFLAKFJFJLAFJLAL
ASDLASKDJASLKDJASLKJFALSKDJALKDJSKLDJLSDKJASLDKJSLDKSDLAKJKS
SILDUAISDALSDJALKDJASDLFATT

I tryed grep -f file_2 file_1 > output but I get only this:

>clat38
>coll9

May I add something more specific to grep?
Thank you for any advice!
Gab

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1 Answer

  1. Editorial Team

    To search for a regular expression on a single line, use grep. Learn it from the man page and a couple of examples.

    To substitute a string for a regular expression on a single line, use sed. Learn it from the man page and a couple of examples.

    For all other text processing applications, use awk. Learn it from the book ” Effective Awk Programming, Third Edition” By Arnold Robbins, http://www.oreilly.com/catalog/awkprog3/.

    awk 'NR==FNR{a[$0];next} $1 in a{c=2} c&&c--' file2 file1

    If you want to print out more than 2 lines when you find the key you want, just change the value of c to 3 or 20 or whatever.

    Given your comment below and your updated sample input, this should do what you want:

    awk 'NR==FNR{a[$0];next} /^>/{f=0} $1 in a{f=1} f' file2 file1
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