User wants "hg19" as genome option

[iskandr]

Email from Wenhui Li:

When I run isovar with parameter " --genome hg19", error occurs. The Error message is the following:

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Traceback (most recent call last):

File "/hwfssz1/ST_PRECISION/USER/liwenhui/01.Software/02.common/anaconda2/bin/isovar-protein-sequences.py", line 4, in

__import__('pkg_resources').run_script('isovar==0.7.0', 'isovar-protein-sequences.py')

File "/hwfssz1/ST_PRECISION/USER/liwenhui/01.Software/02.common/anaconda2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 744, in run_script

File "/hwfssz1/ST_PRECISION/USER/liwenhui/01.Software/02.common/anaconda2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/init.py", line 1506, in run_script

File "/hwfssz1/ST_PRECISION/USER/liwenhui/01.Software/02.common/anaconda2/lib/python2.7/site-packages/isovar-0.7.0-py2.7.egg/EGG-INFO/scripts/isovar-protein-sequences.py", line 46, in

File "build/bdist.linux-x86_64/egg/isovar/cli/protein_sequences.py", line 72, in protein_sequences_dataframe_from_args

File "build/bdist.linux-x86_64/egg/isovar/cli/protein_sequences.py", line 60, in protein_sequences_generator_from_args

File "build/bdist.linux-x86_64/egg/isovar/cli/rna_reads.py", line 79, in allele_reads_generator_from_args

File "/hwfssz1/ST_PRECISION/USER/liwenhui/01.Software/02.common/anaconda2/lib/python2.7/site-packages/varcode-0.5.15-py2.7.egg/varcode/cli/variant_args.py", line 101, in variant_collection_from_args

genome = genome_for_reference_name(args.genome)

File "build/bdist.linux-x86_64/egg/pyensembl/init.py", line 51, in genome_for_reference_name

File "build/bdist.linux-x86_64/egg/pyensembl/species.py", line 138, in normalize_reference_name

ValueError: Reference genome 'hg19' not found

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I want to know how to use the parameter " --genome" to set genome reference (such as Ensembl, or refseq). Would you please to give me some guide? Thank you!

Looking forward to your reply.

Ms. Wenhui Li

Bioinformatics Analyst in BGI, Shenzhen, China