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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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backlocate doesn't find some known 3' mutations #36

Closed bertgold closed 8 years ago

bertgold commented 8 years ago

backlocate appears to have problems locating the following mutation: echo -e "HSD3B2\tP341L" | java -jar dist/backlocate.jar -R hg19.fa It is mutation .0011 here: http://www.omim.org/entry/613890

Alberts-MacBook-Pro:jvarkit bertgold$ echo -e "HSD3B2\tP341L" | java -jar dist/backlocate.jar -R hg19.fa Nov 24, 2015 7:41:01 AM com.github.lindenb.jvarkit.util.command.Command instanceMain INFO: Starting JOB at Tue Nov 24 07:41:01 CST 2015 com.github.lindenb.jvarkit.tools.backlocate.BackLocate version=undefined built=2015-11-21:07-11-51 Nov 24, 2015 7:41:01 AM com.github.lindenb.jvarkit.util.command.Command instanceMain INFO: Command Line args : -R hg19.fa Nov 24, 2015 7:41:01 AM com.github.lindenb.jvarkit.util.command.Command instanceMain INFO: Executing as bertgold@Alberts-MacBook-Pro.local on Mac OS X 10.8.5 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_79-b15 Nov 24, 2015 7:41:02 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri INFO: loading genes Nov 24, 2015 7:41:04 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr17_ctg5_hap1 Nov 24, 2015 7:41:04 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr17_gl000204_random Nov 24, 2015 7:41:04 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr17_gl000205_random Nov 24, 2015 7:41:05 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr19_gl000209_random Nov 24, 2015 7:41:05 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr1_gl000191_random Nov 24, 2015 7:41:05 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr1_gl000192_random Nov 24, 2015 7:41:06 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr4_ctg9_hap1 Nov 24, 2015 7:41:06 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr4_gl000193_random Nov 24, 2015 7:41:06 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr4_gl000194_random Nov 24, 2015 7:41:07 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr6_apd_hap1 Nov 24, 2015 7:41:07 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr6_cox_hap2 Nov 24, 2015 7:41:07 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr6_dbb_hap3 Nov 24, 2015 7:41:07 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr6_mann_hap4 Nov 24, 2015 7:41:07 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr6_mcf_hap5 Nov 24, 2015 7:41:07 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr6_qbl_hap6 Nov 24, 2015 7:41:07 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr6_ssto_hap7 Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr7_gl000195_random Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chr9_gl000201_random Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000211 Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000212 Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000213 Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000214 Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000218 Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000219 Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000220 Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000221 Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000222 Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000223 Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000227 Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000228 Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000229 Nov 24, 2015 7:41:08 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000237 Nov 24, 2015 7:41:09 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000241 Nov 24, 2015 7:41:09 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000243 Nov 24, 2015 7:41:09 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri WARNING: The reference doesn't contain chromosome chrUn_gl000247 Nov 24, 2015 7:41:09 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate loadKnownGenesFromUri INFO: genes:78827 Nov 24, 2015 7:41:09 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 7:41:12 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 7:41:12 AM com.github.lindenb.jvarkit.tools.backlocate.BackLocate call INFO: reading from stdin Nov 24, 2015 7:41:12 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 7:41:12 AM com.github.lindenb.jvarkit.util.command.Command instanceMain SEVERE: java.lang.IndexOutOfBoundsException: Index: 1020, Size: 669 Nov 24, 2015 7:41:12 AM com.github.lindenb.jvarkit.util.command.Command instanceMain SEVERE: Command failed

lindenb commented 8 years ago

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."
bertgold commented 8 years ago

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 bertgold@Alberts-MacBook-Pro.local 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 bertgold@Alberts-MacBook-Pro.local 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$

bertgold commented 8 years ago

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 bertgold@Alberts-MacBook-Pro.local 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 bertgold@Alberts-MacBook-Pro.local 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$

lindenb commented 8 years ago

fixed in https://github.com/lindenb/jvarkit/commit/eac04e587d9e0f784dd1a00c2d1245891a537568

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