Comments (4)
lindenb
commented on September 17, 2024
No problem here....
looking at the format of your logs, you're using an old version of my tool....
$ echo -e "HSD3B2\tP341L" | java -jar dist-1.128/backlocate.jar -R /commun/data/pubdb/broadinstitute.org/bundle/1.5/b37/human_g1k_v37_prefix.fasta
[INFO/BackLocate] 2015-11-24 14:54:45 "Starting JOB at Tue Nov 24 14:54:45 CET 2015 com.github.lindenb.jvarkit.tools.backlocate.BackLocate version=a2c3ee6be5771102726dd0dd83caf9a41574cf3f built=2015-02-23:16-02-16"
[INFO/BackLocate] 2015-11-24 14:54:45 "Command Line args : -R /commun/data/pubdb/broadinstitute.org/bundle/1.5/b37/human_g1k_v37_prefix.fasta"
[INFO/BackLocate] 2015-11-24 14:54:45 "Executing as lindenb@kaamelot-master01 on Linux 2.6.32-431.17.1.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_60-b19"
[WARNING/BackLocate] 2015-11-24 14:54:45 "Undefined knwonGeneURI, using http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz"
[WARNING/BackLocate] 2015-11-24 14:54:45 "Undefined kgXref, using http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/kgXref.txt.gz"
[INFO/BackLocate] 2015-11-24 14:54:45 "loading genes"
[WARNING/BackLocate] 2015-11-24 14:54:50 "The reference doesn't contain chromosome chr17_ctg5_hap1"
[WARNING/BackLocate] 2015-11-24 14:54:53 "The reference doesn't contain chromosome chr4_ctg9_hap1"
[WARNING/BackLocate] 2015-11-24 14:54:53 "The reference doesn't contain chromosome chr6_apd_hap1"
[WARNING/BackLocate] 2015-11-24 14:54:53 "The reference doesn't contain chromosome chr6_cox_hap2"
[WARNING/BackLocate] 2015-11-24 14:54:53 "The reference doesn't contain chromosome chr6_dbb_hap3"
[WARNING/BackLocate] 2015-11-24 14:54:53 "The reference doesn't contain chromosome chr6_mann_hap4"
[WARNING/BackLocate] 2015-11-24 14:54:53 "The reference doesn't contain chromosome chr6_mcf_hap5"
[WARNING/BackLocate] 2015-11-24 14:54:53 "The reference doesn't contain chromosome chr6_qbl_hap6"
[WARNING/BackLocate] 2015-11-24 14:54:53 "The reference doesn't contain chromosome chr6_ssto_hap7"
[INFO/BackLocate] 2015-11-24 14:54:54 "genes:78963"
[INFO/BackLocate] 2015-11-24 14:54:54 "loading http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/kgXref.txt.gz"
[INFO/BackLocate] 2015-11-24 14:55:01 "kgxref:28493"
#User.Gene AA1 petide.pos.1 AA2 knownGene.name knownGene.strand knownGene.AA index0.in.rna codon base.in.rna chromosome index0.in.genomic exon
[INFO/BackLocate] 2015-11-24 14:55:01 "reading from stdin"
[INFO/BackLocate] 2015-11-24 14:55:01 "fetch genome"
#index out of range for :uc001ehu.3 petide length=223
##uc001eht.3
HSD3B2 P 341 L uc001eht.3 + P 1020 CCA C chr1 119965144 Exon 4
HSD3B2 P 341 L uc001eht.3 + P 1021 CCA C chr1 119965145 Exon 4
HSD3B2 P 341 L uc001eht.3 + P 1022 CCA A chr1 119965146 Exon 4
##uc021ost.1
HSD3B2 P 341 L uc021ost.1 + P 1020 CCA C chr1 119965144 Exon 4
HSD3B2 P 341 L uc021ost.1 + P 1021 CCA C chr1 119965145 Exon 4
HSD3B2 P 341 L uc021ost.1 + P 1022 CCA A chr1 119965146 Exon 4
##uc001ehs.3
HSD3B2 P 341 L uc001ehs.3 + P 1020 CCA C chr1 119965144 Exon 3
HSD3B2 P 341 L uc001ehs.3 + P 1021 CCA C chr1 119965145 Exon 3
HSD3B2 P 341 L uc001ehs.3 + P 1022 CCA A chr1 119965146 Exon 3
[INFO/BackLocate] 2015-11-24 14:55:01 "End JOB status=0 [Tue Nov 24 14:55:01 CET 2015] com.github.lindenb.jvarkit.tools.backlocate.BackLocate done. Elapsed time: 0.26 minutes."
from jvarkit.
bertgold
commented on September 17, 2024
I have upgraded and still have the same problem. The program has no difficulty finding 5' mutations in this gene, as you can see below. It is just the ones on the carboxyl terminal end that fail.
Alberts-MacBook-Pro:jvarkit bertgold$ echo -e "HSD3B2\tA10E" | java -jar dist-1.139/backlocate.jar -R hg19.fa
Nov 24, 2015 8:35:25 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Starting JOB at Tue Nov 24 08:35:25 CST 2015 com.github.lindenb.jvarkit.tools.backlocate.BackLocate version=undefined built=2015-11-24:08-11-49
Nov 24, 2015 8:35:25 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Command Line args : -R hg19.fa
Nov 24, 2015 8:35:25 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Executing as [email protected] on Mac OS X 10.8.5 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_79-b15
Nov 24, 2015 8:35:25 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
INFO: loading genes
Nov 24, 2015 8:35:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_ctg5_hap1
Nov 24, 2015 8:35:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_gl000204_random
Nov 24, 2015 8:35:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_gl000205_random
Nov 24, 2015 8:35:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr19_gl000209_random
Nov 24, 2015 8:35:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr1_gl000191_random
Nov 24, 2015 8:35:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr1_gl000192_random
Nov 24, 2015 8:35:30 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_ctg9_hap1
Nov 24, 2015 8:35:30 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_gl000193_random
Nov 24, 2015 8:35:30 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_gl000194_random
Nov 24, 2015 8:35:31 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_apd_hap1
Nov 24, 2015 8:35:31 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_cox_hap2
Nov 24, 2015 8:35:31 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_dbb_hap3
Nov 24, 2015 8:35:31 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_mann_hap4
Nov 24, 2015 8:35:31 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_mcf_hap5
Nov 24, 2015 8:35:31 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_qbl_hap6
Nov 24, 2015 8:35:32 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_ssto_hap7
Nov 24, 2015 8:35:32 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr7_gl000195_random
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr9_gl000201_random
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000211
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000212
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000213
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000214
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000218
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000219
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000220
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000221
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000222
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000223
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000227
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000228
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000229
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000237
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000241
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000243
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000247
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
INFO: genes:78827
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadkgXRefFromUri
INFO: loading http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/kgXref.txt.gz
Nov 24, 2015 8:35:42 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadkgXRefFromUri
INFO: kgxref:28453
#User.Gene AA1 petide.pos.1 AA2 knownGene.name knownGene.strand knownGene.AA index0.in.rna wild.codon potential.var.codons base.in.rna chromosome index0.in.genomic exon
Nov 24, 2015 8:35:42 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate call
INFO: reading from stdin
Nov 24, 2015 8:35:42 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate backLocate
INFO: fetch genome
##uc001ehu.3
HSD3B2 A 10 E uc001ehu.3 + A 27 GCA GAA G chr1 119958069 Exon 2
HSD3B2 A 10 E uc001ehu.3 + A 28 GCA GAA C chr1 119958070 Exon 2
HSD3B2 A 10 E uc001ehu.3 + A 29 GCA GAA A chr1 119958071 Exon 2
##uc001eht.3
HSD3B2 A 10 E uc001eht.3 + A 27 GCA GAA G chr1 119958069 Exon 2
HSD3B2 A 10 E uc001eht.3 + A 28 GCA GAA C chr1 119958070 Exon 2
HSD3B2 A 10 E uc001eht.3 + A 29 GCA GAA A chr1 119958071 Exon 2
##uc021ost.1
HSD3B2 A 10 E uc021ost.1 + A 27 GCA GAA G chr1 119958069 Exon 2
HSD3B2 A 10 E uc021ost.1 + A 28 GCA GAA C chr1 119958070 Exon 2
HSD3B2 A 10 E uc021ost.1 + A 29 GCA GAA A chr1 119958071 Exon 2
##uc001ehs.3
HSD3B2 A 10 E uc001ehs.3 + A 27 GCA GAA G chr1 119958069 Exon 1
HSD3B2 A 10 E uc001ehs.3 + A 28 GCA GAA C chr1 119958070 Exon 1
HSD3B2 A 10 E uc001ehs.3 + A 29 GCA GAA A chr1 119958071 Exon 1
Nov 24, 2015 8:35:43 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: End JOB [Tue Nov 24 08:35:43 CST 2015] BackLocate done. Elapsed time: 0.29 minutes.
Alberts-MacBook-Pro:jvarkit bertgold$ echo -e "HSD3B2\tP341L" | java -jar dist-1.139/backlocate.jar -R hg19.fa
Nov 24, 2015 8:35:59 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Starting JOB at Tue Nov 24 08:35:59 CST 2015 com.github.lindenb.jvarkit.tools.backlocate.BackLocate version=undefined built=2015-11-24:08-11-49
Nov 24, 2015 8:35:59 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Command Line args : -R hg19.fa
Nov 24, 2015 8:35:59 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Executing as [email protected] on Mac OS X 10.8.5 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_79-b15
Nov 24, 2015 8:35:59 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
INFO: loading genes
Nov 24, 2015 8:36:10 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_ctg5_hap1
Nov 24, 2015 8:36:10 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_gl000204_random
Nov 24, 2015 8:36:10 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_gl000205_random
Nov 24, 2015 8:36:12 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr19_gl000209_random
Nov 24, 2015 8:36:12 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr1_gl000191_random
Nov 24, 2015 8:36:12 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr1_gl000192_random
Nov 24, 2015 8:36:16 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_ctg9_hap1
Nov 24, 2015 8:36:16 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_gl000193_random
Nov 24, 2015 8:36:16 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_gl000194_random
Nov 24, 2015 8:36:18 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_apd_hap1
Nov 24, 2015 8:36:18 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_cox_hap2
Nov 24, 2015 8:36:18 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_dbb_hap3
Nov 24, 2015 8:36:18 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_mann_hap4
Nov 24, 2015 8:36:18 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_mcf_hap5
Nov 24, 2015 8:36:18 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_qbl_hap6
Nov 24, 2015 8:36:18 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_ssto_hap7
Nov 24, 2015 8:36:19 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr7_gl000195_random
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr9_gl000201_random
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000211
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000212
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000213
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000214
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000218
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000219
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000220
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000221
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000222
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000223
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000227
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000228
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000229
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000237
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000241
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000243
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000247
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
INFO: genes:78827
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadkgXRefFromUri
INFO: loading http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/kgXref.txt.gz
Nov 24, 2015 8:36:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadkgXRefFromUri
INFO: kgxref:28453
#User.Gene AA1 petide.pos.1 AA2 knownGene.name knownGene.strand knownGene.AA index0.in.rna wild.codon potential.var.codons base.in.rna chromosome index0.in.genomic exon
Nov 24, 2015 8:36:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate call
INFO: reading from stdin
Nov 24, 2015 8:36:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate backLocate
INFO: fetch genome
java.lang.RuntimeException: #index out of range for :uc001ehu.3 petide length=223
at com.github.lindenb.jvarkit.util.command.Command.wrapException(Command.java:252)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.backLocate(BackLocate.java:240)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.run(BackLocate.java:383)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.call(BackLocate.java:531)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.call(BackLocate.java:59)
at com.github.lindenb.jvarkit.util.command.Command.instanceMain(Command.java:546)
at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExit(Command.java:584)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.main(BackLocate.java:566)
java.lang.IndexOutOfBoundsException: Index: 1020, Size: 669
at java.util.ArrayList.rangeCheck(ArrayList.java:635)
at java.util.ArrayList.get(ArrayList.java:411)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate$RNASequence.charAt(BackLocate.java:98)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate$ProteinCharSequence.charAt(BackLocate.java:121)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.backLocate(BackLocate.java:243)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.run(BackLocate.java:383)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.call(BackLocate.java:531)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.call(BackLocate.java:59)
at com.github.lindenb.jvarkit.util.command.Command.instanceMain(Command.java:546)
at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExit(Command.java:584)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.main(BackLocate.java:566)
Nov 24, 2015 8:36:28 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
SEVERE: java.lang.IndexOutOfBoundsException: Index: 1020, Size: 669
Nov 24, 2015 8:36:28 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
SEVERE: Command failed
Alberts-MacBook-Pro:jvarkit bertgold$
from jvarkit.
bertgold
commented on September 17, 2024
I have upgraded, but still have the same problem as you can see below. There is no problem with 5' mutations, but when the mutations are at the 3' end of the gene, the mutation is not found; I am thinking it may be an issue with the ucsc genes you are using.
Alberts-MacBook-Pro:jvarkit bertgold$ echo -e "HSD3B2\tA10E" | java -jar dist-1.139/backlocate.jar -R hg19.fa
Nov 24, 2015 8:35:25 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Starting JOB at Tue Nov 24 08:35:25 CST 2015 com.github.lindenb.jvarkit.tools.backlocate.BackLocate version=undefined built=2015-11-24:08-11-49
Nov 24, 2015 8:35:25 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Command Line args : -R hg19.fa
Nov 24, 2015 8:35:25 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Executing as [email protected] on Mac OS X 10.8.5 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_79-b15
Nov 24, 2015 8:35:25 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
INFO: loading genes
Nov 24, 2015 8:35:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_ctg5_hap1
Nov 24, 2015 8:35:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_gl000204_random
Nov 24, 2015 8:35:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_gl000205_random
Nov 24, 2015 8:35:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr19_gl000209_random
Nov 24, 2015 8:35:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr1_gl000191_random
Nov 24, 2015 8:35:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr1_gl000192_random
Nov 24, 2015 8:35:30 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_ctg9_hap1
Nov 24, 2015 8:35:30 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_gl000193_random
Nov 24, 2015 8:35:30 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_gl000194_random
Nov 24, 2015 8:35:31 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_apd_hap1
Nov 24, 2015 8:35:31 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_cox_hap2
Nov 24, 2015 8:35:31 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_dbb_hap3
Nov 24, 2015 8:35:31 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_mann_hap4
Nov 24, 2015 8:35:31 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_mcf_hap5
Nov 24, 2015 8:35:31 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_qbl_hap6
Nov 24, 2015 8:35:32 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_ssto_hap7
Nov 24, 2015 8:35:32 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr7_gl000195_random
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr9_gl000201_random
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000211
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000212
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000213
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000214
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000218
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000219
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000220
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000221
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000222
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000223
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000227
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000228
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000229
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000237
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000241
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000243
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000247
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
INFO: genes:78827
Nov 24, 2015 8:35:33 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadkgXRefFromUri
INFO: loading http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/kgXref.txt.gz
Nov 24, 2015 8:35:42 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadkgXRefFromUri
INFO: kgxref:28453
#User.Gene AA1 petide.pos.1 AA2 knownGene.name knownGene.strand knownGene.AA index0.in.rna wild.codon potential.var.codons base.in.rna chromosome index0.in.genomic exon
Nov 24, 2015 8:35:42 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate call
INFO: reading from stdin
Nov 24, 2015 8:35:42 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate backLocate
INFO: fetch genome
##uc001ehu.3
HSD3B2 A 10 E uc001ehu.3 + A 27 GCA GAA G chr1 119958069 Exon 2
HSD3B2 A 10 E uc001ehu.3 + A 28 GCA GAA C chr1 119958070 Exon 2
HSD3B2 A 10 E uc001ehu.3 + A 29 GCA GAA A chr1 119958071 Exon 2
##uc001eht.3
HSD3B2 A 10 E uc001eht.3 + A 27 GCA GAA G chr1 119958069 Exon 2
HSD3B2 A 10 E uc001eht.3 + A 28 GCA GAA C chr1 119958070 Exon 2
HSD3B2 A 10 E uc001eht.3 + A 29 GCA GAA A chr1 119958071 Exon 2
##uc021ost.1
HSD3B2 A 10 E uc021ost.1 + A 27 GCA GAA G chr1 119958069 Exon 2
HSD3B2 A 10 E uc021ost.1 + A 28 GCA GAA C chr1 119958070 Exon 2
HSD3B2 A 10 E uc021ost.1 + A 29 GCA GAA A chr1 119958071 Exon 2
##uc001ehs.3
HSD3B2 A 10 E uc001ehs.3 + A 27 GCA GAA G chr1 119958069 Exon 1
HSD3B2 A 10 E uc001ehs.3 + A 28 GCA GAA C chr1 119958070 Exon 1
HSD3B2 A 10 E uc001ehs.3 + A 29 GCA GAA A chr1 119958071 Exon 1
Nov 24, 2015 8:35:43 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: End JOB [Tue Nov 24 08:35:43 CST 2015] BackLocate done. Elapsed time: 0.29 minutes.
Alberts-MacBook-Pro:jvarkit bertgold$ echo -e "HSD3B2\tP341L" | java -jar dist-1.139/backlocate.jar -R hg19.fa
Nov 24, 2015 8:35:59 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Starting JOB at Tue Nov 24 08:35:59 CST 2015 com.github.lindenb.jvarkit.tools.backlocate.BackLocate version=undefined built=2015-11-24:08-11-49
Nov 24, 2015 8:35:59 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Command Line args : -R hg19.fa
Nov 24, 2015 8:35:59 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
INFO: Executing as [email protected] on Mac OS X 10.8.5 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_79-b15
Nov 24, 2015 8:35:59 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
INFO: loading genes
Nov 24, 2015 8:36:10 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_ctg5_hap1
Nov 24, 2015 8:36:10 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_gl000204_random
Nov 24, 2015 8:36:10 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr17_gl000205_random
Nov 24, 2015 8:36:12 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr19_gl000209_random
Nov 24, 2015 8:36:12 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr1_gl000191_random
Nov 24, 2015 8:36:12 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr1_gl000192_random
Nov 24, 2015 8:36:16 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_ctg9_hap1
Nov 24, 2015 8:36:16 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_gl000193_random
Nov 24, 2015 8:36:16 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr4_gl000194_random
Nov 24, 2015 8:36:18 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_apd_hap1
Nov 24, 2015 8:36:18 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_cox_hap2
Nov 24, 2015 8:36:18 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_dbb_hap3
Nov 24, 2015 8:36:18 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_mann_hap4
Nov 24, 2015 8:36:18 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_mcf_hap5
Nov 24, 2015 8:36:18 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_qbl_hap6
Nov 24, 2015 8:36:18 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr6_ssto_hap7
Nov 24, 2015 8:36:19 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr7_gl000195_random
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chr9_gl000201_random
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000211
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000212
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000213
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000214
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000218
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000219
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000220
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000221
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000222
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000223
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000227
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000228
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000229
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000237
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000241
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000243
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
WARNING: The reference doesn't contain chromosome chrUn_gl000247
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri
INFO: genes:78827
Nov 24, 2015 8:36:20 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadkgXRefFromUri
INFO: loading http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/kgXref.txt.gz
Nov 24, 2015 8:36:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadkgXRefFromUri
INFO: kgxref:28453
#User.Gene AA1 petide.pos.1 AA2 knownGene.name knownGene.strand knownGene.AA index0.in.rna wild.codon potential.var.codons base.in.rna chromosome index0.in.genomic exon
Nov 24, 2015 8:36:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate call
INFO: reading from stdin
Nov 24, 2015 8:36:28 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate backLocate
INFO: fetch genome
java.lang.RuntimeException: #index out of range for :uc001ehu.3 petide length=223
at com.github.lindenb.jvarkit.util.command.Command.wrapException(Command.java:252)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.backLocate(BackLocate.java:240)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.run(BackLocate.java:383)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.call(BackLocate.java:531)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.call(BackLocate.java:59)
at com.github.lindenb.jvarkit.util.command.Command.instanceMain(Command.java:546)
at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExit(Command.java:584)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.main(BackLocate.java:566)
java.lang.IndexOutOfBoundsException: Index: 1020, Size: 669
at java.util.ArrayList.rangeCheck(ArrayList.java:635)
at java.util.ArrayList.get(ArrayList.java:411)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate$RNASequence.charAt(BackLocate.java:98)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate$ProteinCharSequence.charAt(BackLocate.java:121)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.backLocate(BackLocate.java:243)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.run(BackLocate.java:383)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.call(BackLocate.java:531)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.call(BackLocate.java:59)
at com.github.lindenb.jvarkit.util.command.Command.instanceMain(Command.java:546)
at com.github.lindenb.jvarkit.util.command.Command.instanceMainWithExit(Command.java:584)
at com.github.lindenb.jvarkit.tools.backlocate.BackLocate.main(BackLocate.java:566)
Nov 24, 2015 8:36:28 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
SEVERE: java.lang.IndexOutOfBoundsException: Index: 1020, Size: 669
Nov 24, 2015 8:36:28 AM com.github.lindenb.jvarkit.util.command.Command instanceMain
SEVERE: Command failed
Alberts-MacBook-Pro:jvarkit bertgold$
from jvarkit.
lindenb
commented on September 17, 2024
fixed in eac04e5
it was a stupid code completion in the new version of my code.
thank you for the report .
BTW, you don't have to call this tool for each variant:
$ echo -e "HSD3B2\tA10E\nHSD3B2\tP341L" | java -jar dist/backlocate.jar -R /commun/data/pubdb/broadinstitute.org/bundle/1.5/b37/human_g1k_v37_prefix.fasta 2> /dev/null
#User.Gene AA1 petide.pos.1 AA2 knownGene.name knownGene.strand knownGene.AA index0.in.rna wild.codon potential.var.codons base.in.rna chromosome index0.in.genomic exon
##uc001ehu.3
HSD3B2 A 10 E uc001ehu.3 + A 27 GCA GAA G chr1 119958069 Exon 2
HSD3B2 A 10 E uc001ehu.3 + A 28 GCA GAA C chr1 119958070 Exon 2
HSD3B2 A 10 E uc001ehu.3 + A 29 GCA GAA A chr1 119958071 Exon 2
##uc001eht.3
HSD3B2 A 10 E uc001eht.3 + A 27 GCA GAA G chr1 119958069 Exon 2
HSD3B2 A 10 E uc001eht.3 + A 28 GCA GAA C chr1 119958070 Exon 2
HSD3B2 A 10 E uc001eht.3 + A 29 GCA GAA A chr1 119958071 Exon 2
##uc021ost.1
HSD3B2 A 10 E uc021ost.1 + A 27 GCA GAA G chr1 119958069 Exon 2
HSD3B2 A 10 E uc021ost.1 + A 28 GCA GAA C chr1 119958070 Exon 2
HSD3B2 A 10 E uc021ost.1 + A 29 GCA GAA A chr1 119958071 Exon 2
##uc001ehs.3
HSD3B2 A 10 E uc001ehs.3 + A 27 GCA GAA G chr1 119958069 Exon 1
HSD3B2 A 10 E uc001ehs.3 + A 28 GCA GAA C chr1 119958070 Exon 1
HSD3B2 A 10 E uc001ehs.3 + A 29 GCA GAA A chr1 119958071 Exon 1
#index out of range for :uc001ehu.3 petide length=223
##uc001eht.3
HSD3B2 P 341 L uc001eht.3 + P 1020 CCA CTA C chr1 119965144 Exon 4
HSD3B2 P 341 L uc001eht.3 + P 1021 CCA CTA C chr1 119965145 Exon 4
HSD3B2 P 341 L uc001eht.3 + P 1022 CCA CTA A chr1 119965146 Exon 4
##uc021ost.1
HSD3B2 P 341 L uc021ost.1 + P 1020 CCA CTA C chr1 119965144 Exon 4
HSD3B2 P 341 L uc021ost.1 + P 1021 CCA CTA C chr1 119965145 Exon 4
HSD3B2 P 341 L uc021ost.1 + P 1022 CCA CTA A chr1 119965146 Exon 4
##uc001ehs.3
HSD3B2 P 341 L uc001ehs.3 + P 1020 CCA CTA C chr1 119965144 Exon 3
HSD3B2 P 341 L uc001ehs.3 + P 1021 CCA CTA C chr1 119965145 Exon 3
HSD3B2 P 341 L uc001ehs.3 + P 1022 CCA CTA A chr1 119965146 Exon 3
from jvarkit.
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