sr2silo.silo

sr2silo.silo.LapisClient

Client for interacting with the Lapis API.

__init__(token_url, submission_url)

Initialize the Lapis client.

authenticate(username, password)

Authenticate with the Lapis API.

submit(group_id, data)

Submit data to the Lapis API.

sr2silo.silo.Submission

Submission-related utilities. Methods for generating placeholder FASTA files containing "NNN" sequences, and S3 links

__init__(fasta, s3_link)

Initialize the Submission object.

generate_placeholder_fasta(submission_ids) staticmethod

Generates a placeholder FASTA file for each submission ID with "NNN" as the sequence.

get_submission_ids_from_tsv(file_path) staticmethod

Reads a TSV file and extracts submission IDs by parsing the "submissionId" column.