| kmkocot |
08-23-2015 07:34 PM |
Need sed help - how to delete all but first two occurrences of a regexp per line
Hi all,
I have a file with many lines that look like this:
Code:
>3|HEMI_Tbah|example|nonsense
MTDFFEKTENQQLVILVTPAGLLQPQLEWPSNLKQKAVYFTRKTKDAVQKDNIRNVLAYGDLSYSPLEQLSALVDEVLVPLLSNPRNHEQWPHVVSQDVLR
>3|HEMI_Tbah|m.2826
ADLKLDLGVQYMKAGVKNIGTVFLMTDAQVADEKFLVLINDLLASGEIPDLFPDEEVENILAGVKNEVKGMGIQDTRENCWKFFIERVRRQLKVVLCFSPVGNTLRVRSRKFPAVVNCTCIDWFHEWPEAALMSVSQRFLEEIDLLDAELKESVAQFMSFVHQSVNEISKVYLANERRYNYTTPKSFLEQIKLYDNLLEMKKKELLQKMDRLENGLTKLQSTASQVDDLKAKLAAQEVELTQKNEDADKLIQIVGVETEKVSKEKAIADDEEKKVAVIAEEVGRKQRDCEADLAKAEPALLAAQEALNTLNKNNLTELKSFGSPPEAVVSVVASVMVLLAPNGKVPKDRSWKAGKIMM
>3|HEMI_Tbah|m.6826
TIPLFPAAVLSYDGKIMMGKVDAFLDQLINYDKENVHENSLKAIRPYLNDPNFEPDFIRNKSGAAAGLCSWVINVIRFYEVYCDVEPKRLALNQANSDLASAQDKLATIKSKITELDANLAELTAKFEAATAAKLKCQQEAESTAKTIELANRLVGGLASENVRWAEAVANFKEQEKTLPGDVLLITAFVSYSGCFIKSYRMELMDEKWLVFLKELKPPIPITENLDPLSLLTDDAAIASWNNEGLPSDRMSTENATILSNCERWPLMIDPQLQGIKWIKKKYGEDLRLVRLGQRGYLDVIERAISSGDTVLIENLEEEMD
>3|HEMI_Tbah|m.20815
AITAGEWPLDKMALQCDVTKKSKEDFSGAPREGSYVHGLYMEGARWDTQTGMLAESRLKELTPAMPVIFIKAIPVDKMETRNIYECPVYKTKDRGPTYVWTFNLKSRDKAARWILGGVALILQV
>3|HEMI_Tbah|m.20028
PILVQRHLSKLFDNMAKLKFEGEAEGEEEEIDSETKVALGMFSKEGEYCDFDNPCECTGQVEVWLNRLQDTMRSTVKFNFSEAVISYEEKPRDQWLFDYAAQVAL
>3|ECHI_Ajap|m.18262
FNPQSFLTAIMQSMARKNEWPLDKMCLQCDVTKKNKEDINSPPREGSYVHGLFMEGARWDTQTGMIADARLKELTPNMPVIFIRAIPVDKQDTRNIYQCPVYKTKQRGPTFVWTFNPKTKEKAAKWTL
>3|ONYC_Oope|cds.c68866_g1_i2|m.4812
KVTAVKIDEARELYRPAAARSSLLYFILGDLYKINPIYQFSLRAFSVVFHKAIERAEQADEVLARVNNLIDCITFSVYIYTTRGLFECDKLIFAAQMTFLILTMAKLIDPQELVIY
The lines that begin with ">" are headers. I want to replace all but the first two occurrences of the pipe symbol ("|") on the headers with underscores ("_"). I know this should be easy with sed and the right combination of 1, 2, and !, but I can't figure it out. Any assistance would be greatly appreciated.
Desired output:
Code:
>3|HEMI_Tbah|example_nonsense
MTDFFEKTENQQLVILVTPAGLLQPQLEWPSNLKQKAVYFTRKTKDAVQKDNIRNVLAYGDLSYSPLEQLSALVDEVLVPLLSNPRNHEQWPHVVSQDVLR
>3|HEMI_Tbah|m.2826
ADLKLDLGVQYMKAGVKNIGTVFLMTDAQVADEKFLVLINDLLASGEIPDLFPDEEVENILAGVKNEVKGMGIQDTRENCWKFFIERVRRQLKVVLCFSPVGNTLRVRSRKFPAVVNCTCIDWFHEWPEAALMSVSQRFLEEIDLLDAELKESVAQFMSFVHQSVNEISKVYLANERRYNYTTPKSFLEQIKLYDNLLEMKKKELLQKMDRLENGLTKLQSTASQVDDLKAKLAAQEVELTQKNEDADKLIQIVGVETEKVSKEKAIADDEEKKVAVIAEEVGRKQRDCEADLAKAEPALLAAQEALNTLNKNNLTELKSFGSPPEAVVSVVASVMVLLAPNGKVPKDRSWKAGKIMM
>3|HEMI_Tbah|m.6826
TIPLFPAAVLSYDGKIMMGKVDAFLDQLINYDKENVHENSLKAIRPYLNDPNFEPDFIRNKSGAAAGLCSWVINVIRFYEVYCDVEPKRLALNQANSDLASAQDKLATIKSKITELDANLAELTAKFEAATAAKLKCQQEAESTAKTIELANRLVGGLASENVRWAEAVANFKEQEKTLPGDVLLITAFVSYSGCFIKSYRMELMDEKWLVFLKELKPPIPITENLDPLSLLTDDAAIASWNNEGLPSDRMSTENATILSNCERWPLMIDPQLQGIKWIKKKYGEDLRLVRLGQRGYLDVIERAISSGDTVLIENLEEEMD
>3|HEMI_Tbah|m.20815
AITAGEWPLDKMALQCDVTKKSKEDFSGAPREGSYVHGLYMEGARWDTQTGMLAESRLKELTPAMPVIFIKAIPVDKMETRNIYECPVYKTKDRGPTYVWTFNLKSRDKAARWILGGVALILQV
>3|HEMI_Tbah|m.20028
PILVQRHLSKLFDNMAKLKFEGEAEGEEEEIDSETKVALGMFSKEGEYCDFDNPCECTGQVEVWLNRLQDTMRSTVKFNFSEAVISYEEKPRDQWLFDYAAQVAL
>3|ECHI_Ajap|m.18262
FNPQSFLTAIMQSMARKNEWPLDKMCLQCDVTKKNKEDINSPPREGSYVHGLFMEGARWDTQTGMIADARLKELTPNMPVIFIRAIPVDKQDTRNIYQCPVYKTKQRGPTFVWTFNPKTKEKAAKWTL
>3|ONYC_Oope|cds.c68866_g1_i2_m.4812
KVTAVKIDEARELYRPAAARSSLLYFILGDLYKINPIYQFSLRAFSVVFHKAIERAEQADEVLARVNNLIDCITFSVYIYTTRGLFECDKLIFAAQMTFLILTMAKLIDPQELVIY
Thank you!
Kevin |
