mgkit.filter.gff_old module

Old GFF filtering module

mgkit.filter.gff_old.choose_annotation(ann1, ann2, threshold, only_same_gene=False, only_same_strand=True, score_func=<function choose_by_score>)

Choos one annotation, based on the score

mgkit.filter.gff_old.choose_by_score(ann1, ann2)

the winner is the first element of the list

mgkit.filter.gff_old.filter_by_bit_score(threshold, annotation)

Filter based on the bit score of the annotation

mgkit.filter.gff_old.filter_by_description(description, annotation)

Filter based on the description of the annotation

mgkit.filter.gff_old.filter_by_hit_length(ko_len, perc, annotation)

Filter based on the its length and the profile length of the annotation

mgkit.filter.gff_old.filter_by_ko_id(ko_ids, annotation)

Filter based on the KO id of the annotation

mgkit.filter.gff_old.filter_by_ko_idx(ko_ids, annotation)

Filter based on the KO id (indexed) of the annotation

mgkit.filter.gff_old.filter_by_reviewed(annotation)

Filter based on the reviewed attribute of the annotation

mgkit.filter.gff_old.filter_by_score(threshold, annotation)

Filter based on the score of the annotation

mgkit.filter.gff_old.filter_by_seq_id(seq_ids, annotation)

Filter based on the sequence containing the annotation

mgkit.filter.gff_old.filter_by_strand(strand, annotation)

Filter based on the strand of the annotation

mgkit.filter.gff_old.filter_by_taxon(taxa, annotation)

Filter based on the taxon name of the annotation

mgkit.filter.gff_old.filter_overlapping(annotations, threshold, same_gene, both_strands, choose_func=<function choose_annotation>, score_func=<function choose_by_score>)

Filters annotations checking how much they overlap, in which case the ones with better score are used.

Parameters:

• annotations (iterable) – iterable of GFF annotations
• threshold (float) – maximum overlap allowed
• same_gene (bool) – if True only filter genes that have the same id
• both_strands (bool) – if True checks annotations on both strands
• choose_func (func) – function used to choose the annotations. Defaults to choose_annotation()
• score_func (func) – function used to decide which annotation to keep if two overlap

Return set:

annotations that passed the filtering