Helpers¶

cblaster.helpers.efetch_sequences(headers)¶

Retrieve protein sequences from NCBI for supplied accessions.

This function uses EFetch from the NCBI E-utilities to retrieve the sequences for all synthases specified in headers. It then calls fasta.parse to parse the returned response; note that extra processing has to occur because the returned FASTA will contain a full sequence description in the header line after the accession.

Parameters:	headers (list) – Valid NCBI sequence identifiers (accession, GI, etc.).

cblaster.helpers.efetch_sequences_request(headers)¶

Launch E-Fetch request for a list of sequence accessions.

Parameters:	headers (list) – NCBI sequence accessions.
Raises:	`requests.HTTPError` – Received bad status code from NCBI.
Returns:	Response returned by requests library.
Return type:	requests.models.Response

cblaster.helpers.form_command(parameters)¶: Flatten a dictionary to create a command list for use in subprocess.run()

cblaster.helpers.get_program_path(aliases)¶

Get programs path given a list of program names.

Parameters:	aliases (list) – Program aliases, e.g. [“diamond”, “diamond-aligner”]
Raises:	`ValueError` – Could not find any of the given aliases on system $PATH.
Returns:	Path to program executable.

cblaster.helpers.get_sequences(query_file=None, query_ids=None)¶

Convenience function to get dictionary of query sequences from file or IDs.

Parameters:	query_file (str) – Path to FASTA file containing query protein sequences. query_ids (list) – NCBI sequence accessions.
Raises:	`ValueError` – Did not receive values for query_file or query_ids.
Returns:	Dictionary of query sequences keyed on accession.
Return type:	sequences (dict)

cblaster.helpers.parse_fasta(handle)¶

Parse sequences in a FASTA file.

Returns:	Sequences in FASTA file keyed on their headers (i.e. > line)