[EMBOSS] Bug in degapseq ?

[Charles Plessy]

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