EcFinder tries to find an EC number for an enzyme name using exact and fuzzy search.
It automatically downloads the EC data file from Expasy.
It can be installed using pip install ec_finder.
The CLI tool ec-find is provided by the package.
The first time the tool is called from the command line, the enzyme
data file is downloaded from Expasy. To update the file if a new file
is available, use ec-find update.
To remove the file (e.g. to force an update), use ec-find cleanup.
Use ec-find "enzyme name" to find the EC number for an enzyme name.
Note the quotes, necessary if there are spaces.
Use ec-find filename 1 to find the EC number for all enzyme names
in a file, where each line contains only an enzyme name each.
Use ec-find filename colnum to find the EC number for all enzyme names
in a Tab-separated file, where enzyme names are in the column with the
specified 1-based column number.
Use ec-find filename colnum --separator S to find the EC number for all
enzyme names in a file separated by separator S.
The first time that ec_finder is imported, the package
data is downloaded from Expasy.
The ec_finder.update() function can be used to check if new
enzyme data is avalaible at Expasy and, if so, download it and update
the data. The ec.finder.cleanup() function deletes the data.
The ec_finder.search(enzyme_name) function is used for searching
for an enzyme name.
The output format consists of three fields, separated by the separator
indicated in the --separator option (CLI), or by the separator argument
of search() (API). By default the Tab is used.
The three fields are:
- result comment
- result EC
- enzyme name (input)
The result comment may be:
- MAIN, the enzyme name was found as one of the main enzye names.
- ALT, the enzyme name was found as one of the alternative enzyme names.
- FUZZY:foobar, the enzyme name was not found, but a similar one (foobar) was found
- NOT_FOUND, the enzyme name was not found (in this case EC is empty)
If the input of the CLI tool ec-find is a file, then each file line
is output after the three fields reported above, separated from it by the
separator (default: tab).
The minimum score for the fuzzy search is by default "90" and can be set
to a value between 0 and 100 by the option --min-score of the CLI
or by the argument min_score of the API function search().
The separator in the output is by default TAB and can be set by
the CLI option --separator (which also changes the input separator,
if the input is a file) or by the API function search() argument
separator.