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pyreference_config_file

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Dave Lawrence edited this page Mar 1, 2023 · 3 revisions

Create a file ~/pyreference.cfg which holds your user settings. Eg:

[global]
default_build=GRCh38

[GRCh37]
genome_accession=GRCh37
genome_sequence_lookup=contig
genes_json=/data/annotation/gene_annotation/refseq/GRCh37/GCF_000001405.25_GRCh37.p13_genomic.105.20220307.gff.json.gz
genome_sequence_fasta=/data/annotation/fasta/GCF_000001405.25_GRCh37.p13_genomic.fna.gz


[GRCh38]
genome_accession=GRCh38
genome_sequence_lookup=contig
genes_json=/data/annotation/gene_annotation/refseq/GRCh38/GCF_000001405.40_GRCh38.p14_genomic.gff.json.gz
genome_sequence_fasta=/data/annotation/fasta/GCF_000001405.40_GRCh38.p14_genomic.fna.gz

This simplifies creating reference objects, eg:

Reference("GRCh37")

is the equivalent of calling:

Reference(genome_accession='GRCh38',
          genome_sequence_lookup='contig',
          genes_json='/data/annotation/gene_annotation/refseq/GRCh38/GCF_000001405.40_GRCh38.p14_genomic.gff.json.gz',
          genome_sequence_fasta='/data/annotation/fasta/GCF_000001405.40_GRCh38.p14_genomic.fna.gz')
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