Crate phcue_ck

Structs

Args

CLI options and arguments

Run

A struct to hold the parsed data from the ENA API and return it to the user

Enums

OutputFormat

Functions

check_num_requests

Validate the total number of concurrent requests to make to the ENA API to make sure it is within the bounds of 1 and 10. If not, return the minimum if num_requests is less than 1 or maximum value if num_requests is larger than 10. We have chosen to bound it to 10 to be nice to the ENA API.

concurrent_query_ena

A function to query the ENA API and return a vector of Run instances This function is used to query the ENA API concurrently across multiple accessions

parse_args

print_csv

A function to handle output in the csv format. This function outputs one read per line.

print_csv_long

A function to handle output in the long csv format. This function prints one variable per line.

print_csv_wide

A function to handle output in the wide csv format. This function outputs one run per line.

read_accessions

A function to read accessions from a file and return a vector of validated accessions. The function skips any empty lines, and will issue a warning if it encounters an invalid accession. This deals with any potential header lines in the file.