Added sleep parameter

--sleep takes the time (in seconds) to wait between requests to UniProt's API

Backwards incompatibility notice: --annotation-columns and --annotation-databases renamed to --columns and --databases, respectively.

Also fixed some bugs in the new namespaces - "output_table" and "columns"

UPIMAPI now easier to handle

Added --output-table option:

• for specifying UniProt info table filename;
• overriding "output" parameter for that file.

Fixed bug in get_ids, now always checks for *

Expanded --full-id parameter, now accepts auto, true and false

• auto - default, if "|" is detected in IDs they are in "full" form
• true - IDs in "full" form
• false - IDs not in "full" form

progressbar replaced with tqdm for a more informative bar

Main report outputted in TSV format

Now outputs UPIMAPI_results in TSV format besides EXCEL

Added new parameters

--evalue: maximum E-value of matches
--pident: minimum percentage of identity
--bitscore: minimum bit score of matches

Joins all information in a single report

Simplified the commands

• Removed --diamond-output: now output is folder where all is stored
• Removed --excel: now EXCEL report is created with all information, as well as TSV report just for UniProt info
• Columns and databases values are now inputed separated by &

Allows an easier connection to KEGGCharter and other tools

Output directories created automatically

Both the directory of --output and the parameter of --diamond-output will be created if not existent.

Now reports time taken in analysis

1.1.3

Now reports time taken in analysis

Max tries now apply to partial lists of IDs

Updated the get_uniprot_information method to take max_tries as input for more robust retrieval of information

• max tries still applies to whole workflow, so three times failed in one interval won't fail the whole workflow

New parameter - max-tries - to set the value of maximum tries for requests from the CLI

Unmapped IDs append to file

Unmapped IDs now do not overwrite previously written unmapped IDs

• instead, append to file

Now with DIAMOND annotation!

UPIMAPI can now be used to perform annotation with DIAMOND, with several improvements:

• threads, block size and number of index chunks can be inputted, or UPIMAPI will automatically determine best values for them
• output from DIAMOND follows directly to UniProt's ID mapping

Also fixed a bug in checking previous mapping with same file name