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synthaser.ncbi

This module handles all interaction with NCBI.

Given a collection of Synthase objects, a workflow might look like:

  1. Launch new CD-Search run

>>> cdsid = ncbi.launch(synthases) >>> cdsid QM3-qcdsearch-B4BAD4B59BC5B80-3E7CFCD3F93E21D0

The query sequences are sent to the batch CD-Search API, where a new run is started and assigned a unique CD-Search identifier (CDSID) which can be used to check on search progress.

Note that search parameters for this search are specified by the values in `SEARCH_PARAMS`:

>>> ncbi.SEARCH_PARAMS { 'db': 'cdd', 'smode': 'auto', 'useid1': 'true', 'compbasedadj': '1', 'filter': 'true', 'evalue': '3.0', 'maxhit': '500', 'dmode': 'full', 'tdata': 'hits' }

which can be freely edited, either directly or by using the set_search_params function.

  1. Poll CD-Search API for results using the CDSID

>>> response = ncbi.retrieve(cdsid)

This function repeatedly polls the API at regular intervals until either results or an error has occurred. Internally, this function calls check(), which takes a CDSID and sends a single request to the API. It returns a Response object (from the requests library), which will have any search content saved in its text or content properties.

>>> print(response.text) #Batch CD-search tool NIH/NLM/NCBI #cdsid QM3-qcdsearch-B4BAD4B59BC5B80-3E7CFCD3F93E21D0 #datatype hitsFull Results #status 0 #Start time 2019-09-03T04:21:23 Run time 0:00:04:23 #status success

  1. Parse results and create Synthase objects

>>> from synthaser import results >>> handle = results.text.split("n") >>> synthases = results.parse(handle)

Additionally, this module provides efetch_sequences, a function for fetching sequences from NCBI from a collection of accessions. For example:

>>> ncbi.efetch_sequences(['CBF71467.1', 'XP_681681.1']) {'CBF71467.1': 'MQSAGMHRATA...', 'XP_681681.1': 'MQDLIAIVGSA...'}

The accessions are sent to the NCBI's Entrez API, which returns the sequences in FASTA format. They are parsed using fasta.parse, and the resulting dictionary is returned.

synthaser.ncbi