Failure to parse well formed clustal file
GoogleCodeExporter opened this issue · comments
WebLogo will not parse the following, well formed clustal file.
'Error: Number of characters in each logo line is not consistent, starting at:
AGO1___SCHPO'
The problem seems to be the last block. If you add gap characters to the last
block so that all
lines are the same length, then the file will parse.
AGO1___SCHPO ----IPKSNPLGN----------VPTLILGGDVYHPGVGATG-----------V---S-I
O02095_CAEEL -----IGSEAFNK----------PNRLIVGFVTSQRVGGNPD-----------Y--PI-S
O16386_CAEEL -----LRSGVFSN----------SKRLIIGFETSQR-GGLGD-----------A--PI-A
O16720_CAEEL --LPNVRPR-IFN----------EPVIFLGCDITHPAAGDTR-----------K--PS-I
O48771_ARATH GIEYSYNIPLINK----------IPTLILGMDVSHGPPGRAD-----------V--PS-V
O62275_CAEEL --------------FVDAKKQL-DSHLIIGVGISAPPAGTKYAMEN---KGVLN--PN-V
O67434_AQUAE -------LKEIEG----------KVDAFVGIDISRITRDGKT-----------------V
O76922_DROME -------QVVIPL----------HGLMTVGFDVCHSPKNKNK-----------S-----
Y
PINH___ARATH VDAISCRIPLVSD----------IPTIIFGADVTHPENGEES-----------S--PS-I
PIWI___ARCFU --------------ILNVDPEK-GSDIIIGTGATRIDNVNLF-----------------C
PIWI___DROME -------MIELPL----------SGLMTIGFDIAKSTRDRKR-----------A-----Y
PIWL1__HUMAN -------RVDIPL----------KLVMIVGIDCYHDMTAGRR-----------S-----I
Q17567_CAEEL -------KVNIPL----------KSTMIVGYDLYHDSTLKGK-----------T-----V
Q19645_CAEEL -ADIPRDLACWNE----------VSTFVIGMDVAHPDRNAAR-------EG--N--PS-
T
Q21495_CAEEL -----VNSETWND----------SGLLLIGLSTAPYLNSYSS-----------E--NVTT
Q21691_CAEEL -VPESVGHRVVCNNSAEMRAKLYAKTQFIGFEMSHTGARTRFDIQKVMFDG--D--PT-
V
Q23415_CAEEL --------------VSDAKKSMTDEQLIIGVGVSAPPAGTKYMMDN---KGHLN--PQ-
I
Q9ZVD5_ARATH SVERTPAFTVISK----------VPTIILGMDVSHGSPGQSD-----------V--PS-I
TAG76__CAEEL IVADKITNKYLVD----------QPTMVVGIDVTHPTQAEMR-----------MNMPS-
V
Y1321__METJA --------------ILDSKT---PYDYIMGLDTGLGIFGNHR-----------------V
YQ53___CAEEL -IPNAVRGKAVCSNNETLRKKLLEHVQFIGFEISHGASRTLFDRSRSQMDG--E--PS-V
AGO1___SCHPO ASIVASVD-LNGCKYTA-VSRSQPR------------HQIPK----SNPLGNVPTLILGG
O02095_CAEEL VGFAANML-KHHQKFAG-GYVYVHR------------DRIGS-----EAFNKPNRLIVGF
O16386_CAEEL IGFAANMM-SHSQQFAG-GYMFVKK------------SALRS-----GVFSNSKRLIIGF
O16720_CAEEL AAVVGSMD-AHPSRYAA-TVRVQQH------------RQLPN---VRPRIFNEPVIFLGC
O48771_ARATH AAVVGSKCWPLISRYRA-AVRTQSP------------RLGIEYSYNIPLINKIPTLILGM
O62275_CAEEL IGYAYNA--QHNQEFSG-DFVLNSA------------SQFVD----AKKQL-DSHLIIGV
O67434_AQUAE NAVAFTKIFNSKGELVR-YYLTSYP----AF------GELKE-------IEGKVDAFVGI
O76922_DROME GAFVATMDQKESFRYFS-TVNEHIK------------GQQVV-------
IPLHGLMTVGF
PINH___ARATH AAVVASQDWPEVTKYAG-LVCAQAH------------RQVDAISCRIPLVSDIPTIIFGA
PIWI___ARCFU FAMVFK---KDGTMLWN-EISPIVT------------SSILN-----VDPEKGSDIIIGT
PIWI___DROME GALIASMDLQQNSTYFS-TVTE-CS------------AFMIE-------LPLSGLMTIGF
PIWL1__HUMAN AGFVASIN-EGMTRWFS-RCIFQDR------------GQRVD-------IPLKLVMIVGI
Q17567_CAEEL GACVSTTS-NDFTQFYS-QTRPHEN------------PTKVN-------IPLKSTMIVGY
Q19645_CAEEL VGLSCNSA-ENPYSFIG-DFLYTDP-------RR---ADIPR---DLACWNEVSTFVIGM
Q21495_CAEEL IGFVSNTM-DHPQKFAG-GYKYVKS------------GSVNS-----ETWNDSGLLLIGL
Q21691_CAEEL VGVAYSL--KHSAQLGGFSYFQESRLVPESVGHRVVCNNSAE----MRAKLYAKTQFIGF
Q23415_CAEEL IGFASNA--VANHEFVG-DFVLAPS------------GQVSD----AKKSMTDEQLIIGV
Q9ZVD5_ARATH AAVVSSREWPLISKYRA-SVRTQPS------------KASVERTPAFTVISKVPTIILGM
TAG76__CAEEL AAIVANVD-LLPQSYGA-NVKVQKK------------CRIVADKITNKYLVDQPTMVVGI
Y1321__METJA GGCTVVY--DSEGKIRR-IQPIETP-AP---------GEILD-------SKTPYDYIMGL
YQ53___CAEEL VGVSYSL--TNSTQLGGFTYLQTQK-IPNAVRGKAVCSNNET----LRKKLLEHVQFIGF
AGO1___SCHPO PVYYAHLVSNLARYQDV
O02095_CAEEL PLYIADRYSQRGAMVLA
O16386_CAEEL PLHIAGTYSERGSQMLA
O16720_CAEEL PAYYAHLVAFRARYHLV
O48771_ARATH PVRYAHLAAAQVAQFTK
O62275_CAEEL PLYVANEYAKRGRNLWN
O67434_AQUAE TVHYSDKITKLMLRGIE
O76922_DROME VCHYAHKLAFLVAESIN
PINH___ARATH PAYYAHLAAFRARFYLE
PIWI___ARCFU TVNYPKLVAGIIANVNR
PIWI___DROME VCQYAKKLATLVGTNLH
PIWL1__HUMAN PCQYAHKLAFLVGQSIH
Q17567_CAEEL PCQYAHKLAFLTAQSLH
Q19645_CAEEL PVYVAHELAKRGTGLYK
Q21495_CAEEL PLYLTAEMAERGTKNLA
Q21691_CAEEL VSYAAQNLAKRGHNNYK
Q23415_CAEEL PLYVANEYAKRGRDLWS
Q9ZVD5_ARATH PICYAHLAAAQLGTFMK
TAG76__CAEEL PVYYADLVATRARCHVK
Y1321__METJA PIHYADKFVKALGKNWK
YQ53___CAEEL VLYAAENLAKRGRNNYK
Original issue reported on code.google.com by GavinCro...@gmail.com
on 4 Mar 2010 at 5:17
Original comment by GavinCro...@gmail.com
on 31 Mar 2010 at 10:22
- Added labels: Milestone-Release3.1
Actually, the real problem may be that this clustal file doesn't have the
customary (but not universal) clustal header line.
Original comment by GavinCro...@gmail.com
on 14 Feb 2011 at 8:20
Fixed in revision 84
Original comment by GavinCro...@gmail.com
on 14 Feb 2011 at 10:04
- Changed state: Fixed
This situation is still happening
Original comment by abi10...@student.lu.se
on 25 Feb 2011 at 6:30