Bio.FSSP.FSSPTools module

Several routines used to extract information from FSSP sections.

filter: filters a passed summary section and alignment section according to a numeric

attribute in the summary section. Returns new summary and alignment sections

For example, to filter in only those records which have a zscore greater than 4.0 and lesser than 7.5:

new_sum, new_align = filter(sum, align, ‘zscore’, 4, 7.5)

class Bio.FSSP.FSSPTools.FSSPAlign(records, alphabet=None, annotations=None, column_annotations=None)

Bases: Bio.Align.MultipleSeqAlignment

Provision to do single Multi Sequence Alignment from FSSP files.

class Bio.FSSP.FSSPTools.FSSPMultAlign

Bases: dict

Provision to do multiple Multi Sequence Alignment from FSSP files.

__init__(self)

Initialize the class.

Bio.FSSP.FSSPTools.mult_align(sum_dict, align_dict)

Return multiple alignment instance (MultipleSeqAlignment).

Bio.FSSP.FSSPTools.filter(sum_dict, align_dict, filter_attribute, low_bound, high_bound)

Filter a passed summary section and alignment section.

Filter according to a numeric attribute in the summary section. Return new summary and alignment sections.

Bio.FSSP.FSSPTools.name_filter(sum_dict, align_dict, name_list)

Filter summary and alignment blocks for given names only.

Accepts a list of names. Returns a new Summary block and Alignment block which contain the info only for those names passed.