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settings.py
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#!/usr/bin/env python3
########################### Description ##################################
# Global values for SeqSender functions
################################################################################
import os
from typing import List, Dict
##### SeqSender settings #####
# Script directory
PROG_DIR: str = os.path.dirname(os.path.abspath(__file__))
# SeqSender version
VERSION: str = "1.1.0 (Beta)"
# Organism options with unique submission options
ORGANISM_CHOICES: List[str] = ["FLU", "COV", "POX", "ARBO", "OTHER"]
# Database submisison options
DATABASE_CHOICES: List[str] = ["BIOSAMPLE", "SRA", "GENBANK", "GISAID"]
# metadata prefix for each database
SAMPLE_NAME_DATABASE_PREFIX: Dict[str, str] = {"BIOSAMPLE":"bs-", "SRA":"sra-", "GENBANK":"gb-", "GISAID":"gs-"}
# Submission status report columns
BIOSAMPLE_SUBMISSION_STATUS_COLUMNS: List[str] = ["biosample_status", "biosample_accession", "biosample_message"]
SRA_SUBMISSION_STATUS_COLUMNS: List[str] = ["sra_status", "sra_accession", "sra_message"]
GENBANK_SUBMISSION_STATUS_COLUMNS: List[str] = ["genbank_status", "genbank_accession", "genbank_message"]
GISAID_SUBMISSION_STATUS_COLUMNS: List[str] = ["gisaid_accession_epi_isl_id", "gisaid_accession_epi_id", "gisaid_message"]
# Upload log columns
SUBMISSION_LOG_COLUMNS: List[str] = ["Submission_Name", "Organism", "Database", "Submission_Type", "Submission_Date", "Submission_ID", "Submission_Status", "Submission_Directory", "Config_File", "Update_Date"]
# Shiny schema options, exclusion list
SCHEMA_EXCLUSIONS = ["config.seqsender.upload_log_schema","config.seqsender.config_file.gisaid_schema","config.seqsender.config_file.ncbi_gisaid_schema", "config.seqsender.config_file.ncbi_schema"]
##### NCBI settings #####
# FTP website to submit samples to
NCBI_FTP_HOST: str = "ftp-private.ncbi.nlm.nih.gov"
# URL structure to download NCBI output files
NCBI_API_URL: str = "https://submit.ncbi.nlm.nih.gov/api/2.0/files/FILE_ID/?format=attachment"
# Table2asn email to submit samples to
TABLE2ASN_EMAIL:str = "[email protected]"
# BioSample metadata regex
BIOSAMPLE_REGEX = "^bs-|^bioproject$|^organism$|^collection_date$"
# SRA metadata regex
SRA_REGEX = "^sra-|^bioproject$|^organism$|^collection_date$"
# Genbank metadata regex
GENBANK_REGEX = "^gb-sample_name$"
# Also added sequence_name to these Genbank entries since I needed it for GISAID, but haven't tested the GenBank workflow yet
# GenBank source file metadata regex
GENBANK_REGEX_SRC = "^sequence_name$|^gb-sample_name$|^src-|^bioproject$|^organism$|^collection_date$"
# GenBank comment file metadata regex
GENBANK_REGEX_CMT = "^sequence_name$|^gb-sample_name$|^cmt-|^organism$|^collection_date$"
##### GISAID settings #####
# GISAID metadata regex
# Added ^sequence_name$ here - it seemed to be getting filtered out too early and causing issues
GISAID_REGEX = "^gs-|^sequence_name$|^collection_date$|^authors$"