thapbi_pict.ena_submit module

Code for sample submission to ENA/SRA.

This implements the thapbi_pict ena-submit ... command.

thapbi_pict.ena_submit.load_md5(file_list: list[str]) → dict[str, str]

Return a dict mapping given filenames to MD5 digests.

thapbi_pict.ena_submit.main(fastq: list[str], output: str, study: str, metadata_file: str | None = None, metadata_encoding: str | None = None, metadata_cols: str | None = None, metadata_fieldnames: str | None = None, metadata_index: str | None = None, ignore_prefixes: str | None = None, library_name: str = '-', instrument_model: str = 'Illumina MiSeq', ignore_stems: str | None = None, tmp_dir: str | None = None, flat: bool = False, debug: bool = False)

Implement the thapbi_pict ena-submit command.

thapbi_pict.ena_submit.write_table(handle, pairs: list[tuple[str, str, str]], meta: dict[str, str] | None, study: str, library_name: str, instrument_model: str, flat: bool = False) → None

Write read file table for ENA upload.

Leave library name as “-” and the folder name will be used.