Bio.Emboss.Primer3 module

Code to parse output from the EMBOSS eprimer3 program.

As elsewhere in Biopython there are two input functions, read and parse, for single record output and multi-record output. For primer3, a single record object is created for each target sequence and may contain multiple primers.

i.e. If you ran eprimer3 with a single target sequence, use the read function. If you ran eprimer3 with multiple targets, use the parse function to iterate over the retsults.

class Bio.Emboss.Primer3.Record

Bases: object

Represent information from a primer3 run finding primers.

Members:

• primers - list of Primer objects describing primer pairs for this target sequence.

• comments - the comment line(s) for the record

__init__(self)

Initialize the class.

class Bio.Emboss.Primer3.Primers

Bases: object

A primer set designed by Primer3.

Members:

• size - length of product, note you can use len(primer) as an alternative to primer.size

• forward_seq

• forward_start

• forward_length

• forward_tm

• forward_gc

• reverse_seq

• reverse_start

• reverse_length

• reverse_tm

• reverse_gc

• internal_seq

• internal_start

• internal_length

• internal_tm

• internal_gc

__init__(self)

Initialize the class.

__len__(self)

Length of the primer product (i.e. product size).

Bio.Emboss.Primer3.parse(handle)

Iterate over primer3 output as Bio.Emboss.Primer3.Record objects.

Bio.Emboss.Primer3.read(handle)

Parse primer3 output into a Bio.Emboss.Primer3.Record object.

This is for when there is one and only one target sequence. If designing primers for multiple sequences, use the parse function.