minorg.filter_grna module

class minorg.filter_grna.Masked(hsp)

Bases: object

__init__(hsp)

property end

property masked

property molecule

property start

within(r, index=0, end_incl=False)

minorg.filter_grna.blast_mask(to_mask_fname, fasta_fname, fout_fname, blastn='blastn', header=['qseqid', 'sseqid', 'mismatch', 'gaps', 'sstart', 'send', 'qstart', 'qend', 'qlen'])

minorg.filter_grna.filter_background_imap(minorg_ifasta_fout_thread_keep)

minorg.filter_grna.filter_background_multiindv(args, threads=1, descr=None)

minorg.filter_grna.make_target_feature_ranges_function(feature_only_ranges, feature_gaps_ranges, max_insertion=15)

minorg.filter_grna.mask_and_generate_outside(mask_fnames, background_fnames=None, mask_reference=True, ref_genes_fasta='', reference_fnames=None, out_dir=None, header=['qseqid', 'sseqid', 'pident', 'length', 'mismatch', 'gaps', 'sstart', 'send', 'qlen', 'slen'], mk_fname=None, blastn='blastn', fout_mask=None, new_file=True, **kwargs)

minorg.filter_grna.mask_identical(to_mask_fname, fasta_fname, fout_fname, **kwargs)

minorg.filter_grna.within_feature(feature_ranges, seq, query_range, min_within_n=1, min_within_fraction=0)