API reference#
This reference is generated from the docstrings of the installed
rotifer package. The data access section is the
curated entry point for the rotifer.db subpackage documented below.
Modules that cannot currently be imported are not listed here; see the issue tracker for the details.
Data access (rotifer.db)#
Access biological sequence and annotation databases. |
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Abstract base class for all database cursors. |
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Mixin classes shared by cursors of the same data type. |
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Cursors that delegate data access to other cursors. |
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Cursors that fetch data using parallel processes. |
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Reusable command line argument sets for database tools. |
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Access NCBI sequence, genome and taxonomy data. |
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Access NCBI databases through the Entrez E-utilities. |
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Access genome data from the NCBI FTP site. |
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Access genome data from a local mirror of the NCBI FTP site. |
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Helper functions for identical protein group (IPG) reports. |
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Access biological data stored on the local machine. |
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Fetch sequences from local FASTA files with Easel. |
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Query the local NCBI Taxonomy database managed by the ETE toolkit. |
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Access biological data stored in SQL databases. |
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Fetch gene neighborhoods and identical protein group reports from local SQLite3 databases. |
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Access data hosted by UniProt. |
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Query UniProt's REST web services. |
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Map database identifiers using UniProt's ID mapping REST service. |
Core infrastructure#
Rapid Open-source Tools and Infrastructure For data Exploration and Research |
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Rotifer's core configuration and setup |
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