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Illumina / hap.py

Haplotype VCF comparison tools
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som.py script not working on examples #76

Open preetida opened 5 years ago

preetida commented 5 years ago

Hi, I have installed hap.py as instructed and running on the example data set. it gives me below error python ~/softwares/hap.py-build/bin/som.py /uufs/chpc.utah.edu/common/home/u0944235/SPIKEinData/ClinVarInjection/BamBlasterFinal/clinvarToInjectB37_edited_included.vcf.gz ../0.001Var_Consensus.all.vcf.gz -f ~/BioApps2/HunterKeith/HSV1_GBM_IDT_Probes_B37Pad25bps.bed -o test File "/uufs/chpc.utah.edu/common/home/u0944235/softwares/hap.py-build/bin/som.py", line 458 print "FP/ambiguity classes with info (multiple classes can " \ ^ SyntaxError: invalid syntax

I can't figure out the error. Any help will be appreciated.

pkrusche commented 5 years ago

Which Python version are you using? hap.py / som.py won't work with Python 3.

preetida commented 5 years ago

Thank you, that worked. I have Lofreq vcfs, that i need to compare with truth file. Does som.py surrports the --roc flag for lofreq ? its not in the option, which option might work with Lofreq, also is there a flag for plotting ? [--roc {varscan2.indel,strelka.snv.qss,mutect.snv,strelka.snv,strelka.indel.evs,varscan2.snv,mutect.indel,strelka.indel,strelka.snv.vqsr}]