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* gh-pages: NCBI importer for recently published whole genomes
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<!-- Import parvovirus genomes sequences from NCBI --> | ||
<ncbiImporter> | ||
<giNumberFieldName>gb_gi_number</giNumberFieldName> | ||
<sequenceFormat>GENBANK_XML</sequenceFormat> | ||
<sourceName>ncbi-new-genomes</sourceName> | ||
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<!-- The eSearchTerm is a standard NCBI entrez text query. | ||
An alternative to eSearchTerm is to specify specific GI numbers or Primary Accessions | ||
to retrieve. See ncbiImporterGiNumbers.xml and ncbiImporterPrimaryAccessions.xml for syntax examples --> | ||
<eSearchTerm>"Parvovirus"[Organism] AND 2000:6000[SLEN] AND 2020/1/1:2024/1/1[Publication Date]</eSearchTerm> | ||
<!-- This specifies the field of the GenBank document which will be used as the GLUE sequence ID. The options are: | ||
GI_NUMBER (default if omitted) | ||
PRIMARY_ACCESSION --> | ||
<sequenceIdField>PRIMARY_ACCESSION</sequenceIdField> | ||
<!-- Maximum number of NCBI records to return. If omitted, defaults to 4000 --> | ||
<eSearchRetMax>1000000</eSearchRetMax> | ||
<!-- Retrieval operates in batches to avoid overloading NCBI. | ||
This is the number of sequences to retrieve per batch --> | ||
<eFetchBatchSize>800</eFetchBatchSize> | ||
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</ncbiImporter> |