malva.search module¶

malva.search.read_sequences_file(file_path)[source]¶

Read sequences from a file (supports FASTA format)

Uses dnaio for efficient and robust parsing of FASTA/FASTQ files.

Parameters:: file_path (str) – Path to the sequence file (FASTA or FASTQ)
Return type:: List[str]
Returns:: List of sequences without headers

malva.search.check_server_connection(server_url)[source]¶

Check if the Malva search server is running

malva.search.submit_search_job(server_url, query, dataset_id=None, include_metadata=False)[source]¶

Submit a search job to the server

malva.search.get_datasets(server_url)[source]¶

Get list of available datasets from the server

malva.search.get_job_status(server_url, job_id)[source]¶

Get status of a job from the server

malva.search.format_results(results, format_type='text')[source]¶

Format search results for output

malva.search.wait_for_completion(server_url, job_id, poll_interval=1)[source]¶

Wait for a job to complete, showing progress