biopython

v1.71.0

biopython v1.71.0 Bio.Restriction.Restriction.FormattedSeq

FormattedSeq(seq, [linear=True])-> new FormattedSeq.

Translate a Bio.Seq into a formatted sequence to be used with Restriction.

Roughly: remove anything which is not IUPAC alphabet and then add a space

     in front of the sequence to get a biological index instead of a
     python index (i.e. index of the first base is 1 not 0).

Retains information about the shape of the molecule linear (default) or circular. Restriction sites are search over the edges of circular sequence.

Link to this section Summary

Functions

__init__()

FormattedSeq(seq, [linear=True])-> new FormattedSeq

circularise()

Circularise sequence in place

finditer()

Return a list of a given pattern which occurs in the sequence

is_linear()

Return if sequence is linear (True) or circular (False)

linearise()

Linearise sequence in place

to_circular()

Make a new instance of sequence as circular

to_linear()

Make a new instance of sequence as linear

Link to this section Functions

Link to this function __init__()

FormattedSeq(seq, [linear=True])-> new FormattedSeq.

seq is either a Bio.Seq, Bio.MutableSeq or a FormattedSeq. if seq is a FormattedSeq, linear will have no effect on the shape of the sequence.

Link to this function circularise()

Circularise sequence in place.

Link to this function finditer()

Return a list of a given pattern which occurs in the sequence.

The list is made of tuple (location, pattern.group). The latter is used with non palindromic sites. Pattern is the regular expression pattern corresponding to the enzyme restriction site. Size is the size of the restriction enzyme recognition-site size.

Link to this function is_linear()

Return if sequence is linear (True) or circular (False).

Link to this function linearise()

Linearise sequence in place.

Link to this function to_circular()

Make a new instance of sequence as circular.

Link to this function to_linear()

Make a new instance of sequence as linear.