Dear developpers, If I use degaspeq on a file, it prompts me for the name of the output, but if the data comes from stdin, degaspeq crashes. It does not happen if the name of the output is given.
chouca〔~〕$ cat toto >Xenopus-1a -----MVLLKCEYRDEEEDLTS---ASPCSV--TSSFRSPAT----QTCSSDDEQLLSPT SP--------------GQHQGEE---NS----------------------------PRCR RSRGRA-QGKSGETVLKIKKTRRVKANNRERNRMHNLNSALDSLREVLPSLPEDAKLTKI ETLRFAYNYIWALSETLRLGD-----P-VHRS--AS-----TPAAAI---LV---QDSSS SQSP-----SWS--CSSSPSS-----S-------CCSFS--PASP----ASST--SDSIE SWQ---PSELHLNPFMSASSA---FI---- >Xenopus-1b -----MVLLKCEYRDEVSELTS---VSPCSVSSSSSHPSPAM----QTCSSDDEQLHSPT SPTL-------THLQQGRDQGEE---NS----------------------------PRCR RSRAR------GDTVLKIKKTRRVKANNRERNRMHHLNYALDSLREVLPSLPEDAKLTKI ETLRFAHNYIWALSETLRLAD-----Q-LHGS--TS-----TPAAAI---LV---QDSYP SLSP-----SWS--CSSSPSS----NS-------CDSFS--PTSP----ASST--SDSIE YWQ---PSELRLNPFMSAL----------- >Gallus-2 ------MPVKAESPAPAAEDE--L-LLLRLASPAPSASLP-------SSAGEEDEDEEDG RP-------------RRLQEGA----------------------------------RRAG RQRGPPRAARTAETAQRIKRSRRLKANNRERNRMHNLNAALDALRDVLPTFPEDAKLTKI ETLRFAHNYIWALTETLRL----AGAARLGGA--AD-A---APGAA-----A---EG-SP SPAS-----SWS--GGASPAP-----SA---SPYACTLS--PGSP----AGSA--SD-AE HW---PPPRGRFAPPPPPHR----CL---- chouca〔~〕$ cat toto | degapseq stdin Removes gap characters from sequences output sequence(s) [xenopus-1a.fasta]: EMBOSS An error in ajmess.c at line 1662: END-OF-FILE reading from user chouca〔~〕$ cat toto | degapseq stdin stdout Removes gap characters from sequences >Xenopus-1a MVLLKCEYRDEEEDLTSASPCSVTSSFRSPATQTCSSDDEQLLSPTSPGQHQGEENSPRC RRSRGRAQGKSGETVLKIKKTRRVKANNRERNRMHNLNSALDSLREVLPSLPEDAKLTKI ETLRFAYNYIWALSETLRLGDPVHRSASTPAAAILVQDSSSSQSPSWSCSSSPSSSCCSF SPASPASSTSDSIESWQPSELHLNPFMSASSAFI >Xenopus-1b MVLLKCEYRDEVSELTSVSPCSVSSSSSHPSPAMQTCSSDDEQLHSPTSPTLTHLQQGRD QGEENSPRCRRSRARGDTVLKIKKTRRVKANNRERNRMHHLNYALDSLREVLPSLPEDAK LTKIETLRFAHNYIWALSETLRLADQLHGSTSTPAAAILVQDSYPSLSPSWSCSSSPSSN SCDSFSPTSPASSTSDSIEYWQPSELRLNPFMSAL >Gallus-2 MPVKAESPAPAAEDELLLLRLASPAPSASLPSSAGEEDEDEEDGRPRRLQEGARRAGRQR GPPRAARTAETAQRIKRSRRLKANNRERNRMHNLNAALDALRDVLPTFPEDAKLTKIETL RFAHNYIWALTETLRLAGAARLGGAADAAPGAAAEGSPSPASSWSGGASPAPSASPYACT LSPGSPAGSASDAEHWPPPRGRFAPPPPPHRCL chouca〔~〕$ degapseq toto Removes gap characters from sequences output sequence(s) [xenopus-1a.fasta]: stdout >Xenopus-1a MVLLKCEYRDEEEDLTSASPCSVTSSFRSPATQTCSSDDEQLLSPTSPGQHQGEENSPRC RRSRGRAQGKSGETVLKIKKTRRVKANNRERNRMHNLNSALDSLREVLPSLPEDAKLTKI ETLRFAYNYIWALSETLRLGDPVHRSASTPAAAILVQDSSSSQSPSWSCSSSPSSSCCSF SPASPASSTSDSIESWQPSELHLNPFMSASSAFI >Xenopus-1b MVLLKCEYRDEVSELTSVSPCSVSSSSSHPSPAMQTCSSDDEQLHSPTSPTLTHLQQGRD QGEENSPRCRRSRARGDTVLKIKKTRRVKANNRERNRMHHLNYALDSLREVLPSLPEDAK LTKIETLRFAHNYIWALSETLRLADQLHGSTSTPAAAILVQDSYPSLSPSWSCSSSPSSN SCDSFSPTSPASSTSDSIEYWQPSELRLNPFMSAL >Gallus-2 MPVKAESPAPAAEDELLLLRLASPAPSASLPSSAGEEDEDEEDGRPRRLQEGARRAGRQR GPPRAARTAETAQRIKRSRRLKANNRERNRMHNLNAALDALRDVLPTFPEDAKLTKIETL RFAHNYIWALTETLRLAGAARLGGAADAAPGAAAEGSPSPASSWSGGASPAPSASPYACT LSPGSPAGSASDAEHWPPPRGRFAPPPPPHRCL Have a nice day, -- Charles Plessy http://charles.plessy.org Wako, Saitama, Japan _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
