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__()
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__()
Initialize the class.
- __len__()
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.