For triggering a feeds importer programmatically -
1) Load the feeds source using feeds_source() - by passing argument importer id [it is the machine name of the importer; you can find it in the table 'feeds_source']
$feeds_source = feeds_source([importer_id]);
2) Set up the configuration -
$feeds_config = $feeds_source->getConfigFor($feeds_source->importer->fetcher);
$feeds_config['source'] = $url;//url of file | url of site
3) Set configurations to feeds source
4) Start the import
I have implemented this for fetching data from url. Haven't tried with file, but this should work with may be some minor changes in the config part.
Else I think you can trigger the feeds using cron too. Elysia Cron is a great module which gives 'fine grain control over each task and several ways to add custom cron jobs to your site'.
I hope this is of help.