AccessoryFunctions Overview
AccessoryFunctions contains miscellaneous methods that don't necessarily fit anywhere else. They may be useful.
Download File
from accessoryFunctions import accessoryFunctions
accessoryFunctions.download_file(address, output_name, hour_start=18, hour_end=6, day_start=5, day_end=6, timeout=600)
This method will allow for file downloads between specified hours (default 6PM to 6AM) or on specified days (default Saturday and Sunday). The address
argument must the URL for a single file, not a folder.
If the download is interrupted by the end of the download window, it will be continued when the download window reopens.
IMPORTANT: output_name
must be an absolute path, and for whatever reason curl doesn't like the ~ character, so it can't be used in this command.
Make Path
from accessoryFunctions import accessoryFunctions
accessoryFunctions.make_path(inpath)
Simple method to make a directory if it doesn't already exist. Only argument is the directory you want to create.
Print Time
from accessoryFunctions import accessoryFunctions
accessoryFunctions.printtime(string, start)
Prints out elapsed time since start
, followed by the text contained in string
. Prints it out in bold, so it looks good!
Dependency Check
from accessoryFunctions import accessoryFunctions
present = accessoryFunctions.dependency_check(dependency)
Not sure if a program required in your script is installed and on the $PATH? Use this method to check for you - it will return True
if the program is present, and False
if it isn't.
A good way to warn users of your scripts that not everything needed is installed.
NOTE: Doesn't check the version of the program, so don't rely on it for that.
Find Paired Reads
from accessoryFunctions import accessoryFunctions
pairs = accessoryFunctions.find_paired_reads(directory, forward_id='_R1', reverse_id='_R2')
This method will look into the directory specified with the directory
argument and return a list of files that appear to be read pairs. Default forward and reverse identifiers are '_R1' and '_R2', respectively, but these can be changed with the forward_id
and reverse_id
keyword arguments.
The return will be a nested list with the following format: [[forward_1, reverse_1], [forward_2, reverse_2]], and so on.