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spond / IgSCUEAL

B-cell 454 processing
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AuxBF/SplitIMGTV.bf throws an error #3

Closed sdwfrost closed 9 years ago

sdwfrost commented 9 years ago

Using the latest HyPhy from veg/hyphy:

$ HYPHYMP AuxBF/SplitIMGTV.bf

AuxBF/IMGT V-region protein alignment:homo_sapiens/ighv_imgt_aa.txt
Regular expression to filter annotation with (e.g. F for functional, F|ORF for function or ORF):F
Error:
Operation 'MAccess' is not implemented/defined for a Number

Function call stack
1 : Branch under condition 'match[0]==0&&match[1]==Abs(annotation[5])-1'
    to
        v_region=imgt_aa[k+1]^{{"\\.",""}}
    else
        k+=2
-------
Segmentation fault
spond commented 9 years ago

Hi Simon,

I can't reproduce this bug (see issue3.txt in test as my sample input). Please push the input file to "test" so I can track down the problem.

Sergei

sdwfrost commented 9 years ago

Your issue3.txt looks the same as mine. Using your issue3.txt, I get the following warnings

Sequence QVQLVQSGA.EVKKP GASVKVSCKAS GYTF....TGYY MHWVRQAP GQGLEWMGR INPN..SGGT NYAQKFQ.G RVTSTRDTSI STAYMELSRLRS DDTVVYYC AR  contained 0 space-separated blocks (expected 11) and has been skipped
Sequence QVQLVQSGA.EVKKP GASVKVSCKAS GYTF....TSYA MHWVRQAP GQRLEWMGW INAG..NGNT KYSQKFQ.G RVTITRDTSA STAYMELSSLRS EDTAVYYC AR  contained 0 space-separated blocks (expected 11) and has been skipped
Sequence QVQLVQSGA.EVKKP GASVKVSCKAS GYTF....TSYD INWVRQAT GQGLEWMGW MNPN..SGNT GYAQKFQ.G RVTMTRNTSI STAYMELSSLRS EDTAVYYC AR  contained 0 space-separated blocks (expected 11) and has been skipped
Sequence QVQLVQSGA.EVKKP GASVKVSCKAS GYTF....TSYG ISWVRQAP GQGLEWMGW ISAY..NGNT NYAQKLQ.G RVTMTTDTST STAYMELRSLRS DDTAVYYC AR  contained 0 space-separated blocks (expected 11) and has been skipped
Sequence QVQLVQSGA.EVKKP GASVKVSCKVS GYTL....TELS MHWVRQAP GKGLEWMGG FDPE..DGET IYAQKFQ.G RVTMTEDTST DTAYMELSSLRS EDTAVYYC AT  contained 0 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV1-38-4  IGHV1-38-4*01   KF698736    VH  ORF  did not match the functional filter and has been skipped
Sequence QMQLVQSGA.EVKKT GSSVKVSCKAS GYTF....TYRY LHWVRQAP GQALEWMGW ITPF..NGNT NYAQKFQ.D RVTITRDRSM STAYMELSSLRS EDTAMYYC AR  contained 0 space-separated blocks (expected 11) and has been skipped
Sequence QVQLVQSGA.EVKKP GASVKVSCKAS GYTF....TSYY MHWVRQAP GQGLEWMGI INPS..GGST SYAQKFQ.G RVTMTRDTST STVYMELSSLRS EDTAVYYC AR  contained 0 space-separated blocks (expected 11) and has been skipped
Sequence QMQLVQSGP.EVKKP GTSVKVSCKAS GFTF....TSSA VQWVRQAR GQRLEWIGW IVVG..SGNT NYAQKFQ.E RVTITRDMST STAYMELSSLRS EDTAVYYC AA  contained 0 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV1-68    IGHV1-68*01 AB019437    VH  P    did not match the functional filter and has been skipped
Sequence QVQLVQSGA.EVKKP GSSVKVSCKAS GGTF....SSYA ISWVRQAP GQGLEWMGG IIPI..FGTA NYAQKFQ.G RVTITADEST STAYMELSSLRS EDTAVYYC AR  contained 0 space-separated blocks (expected 11) and has been skipped
Sequence EVQLVQSGA.EVKKP GATVKISCKVS GYTF....TDYY MHWVQQAP GKGLEWMGL VDPE..DGET IYAEKFQ.G RVTITADTST DTAYMELSSLRS EDTAVYYC AT  contained 0 space-separated blocks (expected 11) and has been skipped
Sequence QVQLVQSGA.EVKKP GSSVKVSCKAS GGTF....SSYA ISWVRQAP GQGLEWMGG IIPI..FGTA NYAQKFQ.G RVTITADEST STAYMELSSLRS EDTAVYYC AR  contained 0 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV1-NL1   IGHV1-NL1*01    M13911  VH  P    did not match the functional filter and has been skipped
Sequence Homsap IGHV2-10    IGHV2-10*01 M99647  VH  P    did not match the functional filter and has been skipped
Sequence EVQLVESGG.GLVQP GGSLRLSCAAS GFTF....SSYW MSWVRQAP GKGLEWVAN IKQD..GSEK YYVDSVK.G RFTISRDNAK NSLYLQMNSLRA EDTAVYYC AR  contained 3 space-separated blocks (expected 11) and has been skipped
Sequence QVQLVESGG.GLVKP GGSLRLSCAAS GFTF....SDYY MSWIRQAP GKGLEWVSY ISSS..GSTI YYADSVK.G RFTISRDNAK NSLYLQMNSLRA EDTAVYYC AR  contained 4 space-separated blocks (expected 11) and has been skipped
Sequence EVQLVESGG.GLVQP GGSLRLSCAAS GFTF....SSYD MHWVRQAT GKGLEWVSA IGTA...GDT YYPGSVK.G RFTISRENAK NSLYLQMNSLRA GDTAVYYC AR  contained 4 space-separated blocks (expected 11) and has been skipped
Sequence EVQLVESGG.GLVKP GGSLRLSCAAS GFTF....SNAW MSWVRQAP GKGLEWVGR IKSKTDGGTT DYAAPVK.G RFTISRDDSK NTLYLQMNSLKT EDTAVYYC TT  contained 4 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV3-16    IGHV3-16*01 M99655  VH  ORF  did not match the functional filter and has been skipped
Sequence Homsap IGHV3-19    IGHV3-19*01 M99656  VH  P    did not match the functional filter and has been skipped
Sequence EVQLVESGG.GVVRP GGSLRLSCAAS GFTF....DDYG MSWVRQAP GKGLEWVSG INWN..GGST GYADSVK.G RFTISRDNAK NSLYLQMNSLRA EDTALYHC AR  contained 4 space-separated blocks (expected 11) and has been skipped
Sequence EVQLVESGG.GLVKP GGSLRLSCAAS GFTF....SSYS MNWVRQAP GKGLEWVSS ISSS..SSYI YYADSVK.G RFTISRDNAK NSLYLQMNSLRA EDTAVYYC AR  contained 4 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV3-22    IGHV3-22*01 M99659  VH  P    did not match the functional filter and has been skipped
Sequence EVQLLESGG.GLVQP GGSLRLSCAAS GFTF....SSYA MSWVRQAP GKGLEWVSA ISGS..GGST YYADSVK.G RFTISRDNSK NTLYLQMNSLRA EDTAVYYC AK  contained 4 space-separated blocks (expected 11) and has been skipped
Sequence EVQLLESGG.GLVQP GGSLRLSCAAS GFTF....SSYA MSWVRQAP GKGLEWVSA ISGS..GGST YYADSVK.G RFTISRDNSK NTLYLQMNSLRA EDTAVYYC AK  contained 4 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV3-25    IGHV3-25*01 M99661  VH  P    did not match the functional filter and has been skipped
Sequence Homsap IGHV3-29    IGHV3-29*01 AB019439    VH  P    did not match the functional filter and has been skipped
Sequence QVQLVESGG.GVVQP GRSLRLSCAAS GFTF....SSYA MHWVRQAP GKGLEWVAV ISYD..GSNK YYADSVK.G RFTISRDNSK NTLYLQMNSLRA EDTAVYYC AR  contained 4 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV3-30-2  IGHV3-30-2*01   AB019439    VH  P    did not match the functional filter and has been skipped
Sequence QVQLVESGG.GVVQP GRSLRLSCAAS GFTF....SSYA MHWVRQAP GKGLEWVAV ISYD..GSNK YYADSVK.G RFTISRDNSK NTLYLQMNSLRA EDTAVYYC AR  contained 4 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV3-32    IGHV3-32*01 AB019439    VH  P    did not match the functional filter and has been skipped
Sequence QVQLVESGG.GVVQP GRSLRLSCAAS GFTF....SSYG MHWVRQAP GKGLEWVAV IWYD..GSNK YYADSVK.G RFTISRDNSK NTLYLQMNSLRA EDTAVYYC AR  contained 4 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV3-33-2  IGHV3-33-2*01   AB019439    VH  P    did not match the functional filter and has been skipped
Sequence Homsap IGHV3-35    IGHV3-35*01 M99666  VH  ORF  did not match the functional filter and has been skipped
Sequence Homsap IGHV3-38    IGHV3-38*01 M99669  VH  ORF  did not match the functional filter and has been skipped
Sequence Homsap IGHV3-38-3  IGHV3-38-3*01   KF698732    VH  ORF  did not match the functional filter and has been skipped
Sequence Homsap IGHV3-47    IGHV3-47*01 Z18900  VH  P    did not match the functional filter and has been skipped
Sequence EVQLVESGG.GLVQP GGSLRLSCAAS GFTF....SSYS MNWVRQAP GKGLEWVSY ISSS..SSTI YYADSVK.G RFTISRDNAK NSLYLQMNSLRA EDTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence EVQLVESGG.GLVQP GRSLRLSCTAS GFTF....GDYA MSWFRQAP GKGLEWVGF IRSKAYGGTT EYTASVK.G RFTISRDGSK SIAYLQMNSLKT EDTAVYYC TR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV3-52    IGHV3-52*01 M99678  VH  P    did not match the functional filter and has been skipped
Sequence EVQLVESGG.GLIQP GGSLRLSCAAS GFTV....SSNY MSWVRQAP GKGLEWVSV IYSG...GST YYADSVK.G RFTISRDNSK NTLYLQMNSLRA EDTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV3-54    IGHV3-54*01 M99680  VH  P    did not match the functional filter and has been skipped
Sequence Homsap IGHV3-62    IGHV3-62*01 AB019437    VH  P    did not match the functional filter and has been skipped
Sequence Homsap IGHV3-63    IGHV3-63*01 M99681  VH  P    did not match the functional filter and has been skipped
Sequence EVQLVESGG.GLVQP GGSLRLSCAAS GFTF....SSYA MHWVRQAP GKGLEYVSA ISSN..GGST YYANSVK.G RFTISRDNSK NTLYLQMGSLRA EDMAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence EVQLVESGG.GLVQP GGSLRLSCAAS GFTV....SSNY MSWVRQAP GKGLEWVSV IYSG...GST YYADSVK.G RFTISRDNSK NTLYLQMNSLRA EDTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV3-69-1  IGHV3-69-1*01   AJ879484    VH  P    did not match the functional filter and has been skipped
Sequence Homsap IGHV3-71    IGHV3-71*01 AB019437    VH  P    did not match the functional filter and has been skipped
Sequence EVQLVESGG.GLVQP GGSLRLSCAAS GFTF....SDHY MDWVRQAP GKGLEWVGR TRNKANSYTT EYAASVK.G RFTISRDDSK NSLYLQMNSLKT EDTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence EVQLVESGG.GLVQP GGSLKLSCAAS GFTF....SGSA MHWVRQAS GKGLEWVGR IRSKANSYAT AYAASVK.G RFTISRDDSK NTAYLQMNSLKT EDTAVYYC TR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence EVQLVESGG.GLVQP GGSLRLSCAAS GFTF....SSYW MHWVRQAP GKGLVWVSR INSD..GSST SYADSVK.G RFTISRDNAK NTLYLQMNSLRA EDTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence QVQLVESGG.GVVQP GGSLRLSCAAS GFTF....SSYG MHWVRQAP GKGLEWVSV IYSG..GSST YYADSVK.G RFTISRDNSK NTLYLQMNSLRA EDTAVYYC AK  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence QVQLQESGP.GLVKP PGTLSLTCAVS GGSIS...SSNW WSWVRQPP GKGLEWIGE IYHS...GST NYNPSLK.S RVTISVDKSK NQFSLKLSSVTA ADTAVYCC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence QVQLQESGP.GLVKP SDTLSLTCAVS GYSIS...SSNW WGWIRQPP GKGLEWIGY IYYS...GST YYNPSLK.S RVTMSVDTSK NQFSLKLSSVTA VDTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence QLQLQESGS.GLVKP SQTLSLTCAVS GGSIS..SGGYS WSWIRQPP GKGLEWIGY IYHS...GST YYNPSLK.S RVTISVDRSK NQFSLKLSSVTA ADTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence QVQLQESGP.GLVKP SQTLSLTCTVS GGSIS..SGDYY WSWIRQPP GKGLEWIGY IYYS...GST YYNPSLK.S RVTISVDTSK NQFSLKLSSVTA ADTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence QVQLQESGP.GLVKP SQTLSLTCTVS GGSIS..SGGYY WSWIRQHP GKGLEWIGY IYYS...GST YYNPSLK.S LVTISVDTSK NQFSLKLSSVTA ADTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence QVQLQQWGA.GLLKP SETLSLTCAVY GGSF....SGYY WSWIRQPP GKGLEWIGE INHS...GST NYNPSLK.S RVTISVDTSK NQFSLKLSSVTA ADTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence QVQLQESGP.GLVKP SETLSLTCAVS GYSIS...SGYY WGWIRQPP GKGLEWIGS IYHS...GST YYNPSLK.S RVTISVDTSK NQFSLKLSSVTA ADTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence QLQLQESGP.GLVKP SETLSLTCTVS GGSIS..SSSYY WGWIRQPP GKGLEWIGS IYYS...GST YYNPSLK.S RVTISVDTSK NQFSLKLSSVTA ADTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV4-55    IGHV4-55*01 M99685  VH  P    did not match the functional filter and has been skipped
Sequence QVQLQESGP.GLVKP SETLSLTCTVS GGSI....SSYY WSWIRQPP GKGLEWIGY IYYS...GST NYNPSLK.S RVTISVDTSK NQFSLKLSSVTA ADTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence QVQLQESGP.GLVKP SETLSLTCTVS GGSVS..SGSYY WSWIRQPP GKGLEWIGY IYYS...GST NYNPSLK.S RVTISVDTSK NQFSLKLSSVTA ADTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence EVQLVQSGA.EVKKP GESLRISCKGS GYSF....TSYW ISWVRQMP GKGLEWMGR IDPS..DSYT NYSPSFQ.G HVTISADKSI STAYLQWSSLKA SDTAMYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence EVQLVQSGA.EVKKP GESLKISCKGS GYSF....TSYW IGWVRQMP GKGLEWMGI IYPG..DSDT RYSPSFQ.G QVTISADKSI STAYLQWSSLKA SDTAMYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV5-78    IGHV5-78*01 X92213  VH  P    did not match the functional filter and has been skipped
Sequence QVQLQQSGP.GLVKP SQTLSLTCAIS GDSVS..SNSAA WNWIRQSP SRGLEWLGR TYYRS.KWYN DYAVSVK.S RITINPDTSK NQFSLQLNSVTP EDTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence QVQLVQSGS.ELKKP GASVKVSCKAS GYTF....TSYA MNWVRQAP GQGLEWMGW INTN..TGNP TYAQGFT.G RFVFSLDTSV STAYLQICSLKA EDTAVYYC AR  contained 6 space-separated blocks (expected 11) and has been skipped
Sequence Homsap IGHV7-34-1  IGHV7-34-1*01   AB019439    VH  P    did not match the functional filter and has been skipped
Sequence Homsap IGHV7-81    IGHV7-81*01 AB019437    VH  ORF  did not match the functional filter and has been skipped

These are the same warnings as my text file - my HYPHYMP is up to date too. I'm doing this on Linux...

spond commented 9 years ago

Fixed with 02bdce33f6bb920a42c66070320cbda3a2d868dd