mgkit.consts module

Module containing constants for the filter package

mgkit.consts.BLACK_LIST = ['bos', 'pecora', 'lolium', 'streptophyta', 'oryza', 'fabales', 'poaceae', 'metazoa', 'chlorophyta']

Default taxa black list, includes all taxa names that are to be excluded from some analysis.

mgkit.consts.DEFAULT_SNP_FILTER = {'black_list': [903, 35500, 4520, 35493, 4527, 72025, 4479, 33208, 3041], 'func': <function is_ancestor>, 'include_only': [2157, 2, 4751, 33630, 554915, 554296, 1401294, 193537, 28009, 5738, 33682, 207245, 5752, 556282, 136087, 66288, 5719, 543769], 'min_cov': 4}

Default filter options for filtering mgkit.snps.GeneSyn

mgkit.consts.MIN_COV = 4

Minumum coverage required in some functions.

mgkit.consts.MIN_NUM = 10

Used to set the minimum number of replicates for some functions