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am = vvhgvs.assemblymapper.AssemblyMapper(hdp, assembly_name='GRCh37', alt_aln_method='splign', replace_reference=True) transcripts = am.relevant_transcripts(var_g) #6

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mashok-acog opened this issue Oct 6, 2022 · 1 comment
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am = vvhgvs.assemblymapper.AssemblyMapper(hdp, assembly_name='GRCh37', alt_aln_method='splign', replace_reference=True) transcripts = am.relevant_transcripts(var_g) #6

mashok-acog opened this issue Oct 6, 2022 · 1 comment

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@mashok-acog
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mashok-acog commented Oct 6, 2022 •
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transcripts = am.relevant_transcripts(var_g)
psycopg2.errors.UndefinedTable: relation "current_valid_mapped_transcript_spans_mv" does not exist
LINE 3: from current_valid_mapped_transcript_spans_mv
@mashok-acog mashok-acog changed the title AssemblyMapper throws an error am = vvhgvs.assemblymapper.AssemblyMapper(hdp, assembly_name='GRCh37', alt_aln_method='splign', replace_reference=True) # identify transcripts that overlap this genomic variant >>> transcripts = am.relevant_transcripts(var_g) Oct 6, 2022
@mashok-acog mashok-acog changed the title am = vvhgvs.assemblymapper.AssemblyMapper(hdp, assembly_name='GRCh37', alt_aln_method='splign', replace_reference=True) # identify transcripts that overlap this genomic variant >>> transcripts = am.relevant_transcripts(var_g) am = vvhgvs.assemblymapper.AssemblyMapper(hdp, assembly_name='GRCh37', alt_aln_method='splign', replace_reference=True) \n transcripts = am.relevant_transcripts(var_g) Oct 6, 2022
@mashok-acog mashok-acog changed the title am = vvhgvs.assemblymapper.AssemblyMapper(hdp, assembly_name='GRCh37', alt_aln_method='splign', replace_reference=True) \n transcripts = am.relevant_transcripts(var_g) am = vvhgvs.assemblymapper.AssemblyMapper(hdp, assembly_name='GRCh37', alt_aln_method='splign', replace_reference=True) transcripts = am.relevant_transcripts(var_g) Oct 6, 2022
@mashok-acog
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@John-F-Wagstaff , Thanx for the response, I made the changes you suggested and it is working like a charm. Made VariantValidator point to VVTA Database and executed the script. It works !

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