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License: GNU General Public License v3.0
Predicting alternative splicing change caused by genetic mutations
License: GNU General Public License v3.0
I installed libsvm 3.32 and got this error with PredPSI-SVM
./main.sh example/sample.vcf -o example/outdir
>>== Check commands availablity ==<<
/usr/bin/python
/usr/bin/python3
/usr/bin/perl
/usr/bin/samtools
** ERROR: check variable "svm_scale" in src/init.sh
** ERROR: check variable "svm_predict" in src/init.sh
** ANNOVAR annotating......
NOTICE: Finished reading 99 lines from VCF file
NOTICE: A total of 99 locus in VCF file passed QC threshold, representing 99 SNPs (77 transitions and 22 transversions) and 0 indels/substitutions
NOTICE: Finished writting 0 SNPs (0 transitions and 0 transversions) and 0 indels/substitutions for 1 sample
NOTICE: The --geneanno operation is set to ON by default
NOTICE: Reading gene annotation from /data/jess_tmp/fh/PredPSI-SVR/tools/annovar/humandb/hg19_ensGene.txt ... Done with 103433 transcripts (including 38799 without coding sequence annotation) for 47132 unique genes
NOTICE: Finished gene-based annotation on 0 genetic variants in /data/jess_tmp/fh/PredPSI-SVR/example/outdir/input.avinput
NOTICE: Output files were written to /data/jess_tmp/fh/PredPSI-SVR/example/outdir/annovar.variant_function, /data/jess_tmp/fh/PredPSI-SVR/example/outdir/annovar.exonic_variant_function
DONE
** Preparing mutation info...
- only vcf, finding exon transcript...
/data/jess_tmp/fh/PredPSI-SVR/src/utils.py:30: SyntaxWarning: "is" with a literal. Did you mean "=="?
assert errmsg is '', "Error in file 'utils.py':'get_genome': " + errmsg
/data/jess_tmp/fh/PredPSI-SVR/src/utils.py:51: SyntaxWarning: "is" with a literal. Did you mean "=="?
if len(args) is 0:
/data/jess_tmp/fh/PredPSI-SVR/src/utils.py:118: SyntaxWarning: "is" with a literal. Did you mean "=="?
if self.strand is '-':
/data/jess_tmp/fh/PredPSI-SVR/src/utils.py:292: SyntaxWarning: "is" with a literal. Did you mean "=="?
if strand is '+':
However, you can fix it by doing
chmod -x svm-predict.c
chmod -x svm-scale.c
And change all the "is" in util.py to "=="
This gives
./main.sh example/sample.vcf -o example/outdir
>>== Check commands availablity ==<<
/usr/bin/python
/usr/bin/python3
/usr/bin/perl
/usr/bin/samtools
/data/jess_tmp/fh/PredPSI-SVR/tools/libsvm-3.32/svm-scale.c
/data/jess_tmp/fh/PredPSI-SVR/tools/libsvm-3.32/svm-predict.c
** ANNOVAR annotating......
NOTICE: Finished reading 99 lines from VCF file
NOTICE: A total of 99 locus in VCF file passed QC threshold, representing 99 SNPs (77 transitions and 22 transversions) and 0 indels/substitutions
NOTICE: Finished writting 0 SNPs (0 transitions and 0 transversions) and 0 indels/substitutions for 1 sample
NOTICE: The --geneanno operation is set to ON by default
NOTICE: Reading gene annotation from /data/jess_tmp/fh/PredPSI-SVR/tools/annovar/humandb/hg19_ensGene.txt ... Done with 103433 transcripts (including 38799 without coding sequence annotation) for 47132 unique genes
NOTICE: Finished gene-based annotation on 0 genetic variants in /data/jess_tmp/fh/PredPSI-SVR/example/outdir/input.avinput
NOTICE: Output files were written to /data/jess_tmp/fh/PredPSI-SVR/example/outdir/annovar.variant_function, /data/jess_tmp/fh/PredPSI-SVR/example/outdir/annovar.exonic_variant_function
DONE
** Preparing mutation info...
- only vcf, finding exon transcript...
I haven't got OUTPUT.dpsi but that might be because I haven't got the SPIDEX database installed yet (still waiting for a link)
/PredPSI-SVR/example/outdir$ ls
annovar.exonic_variant_function annovar.log annovar.variant_function input.avinput input.vcf mut_info mut_info.valid
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