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.
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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
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__init__
(self)¶ Initialize the class.
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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
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__init__
(self)¶ Initialize the class.
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__len__
(self)¶ Length of the primer product (i.e. product size).
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Bio.Emboss.Primer3.
parse
(handle)¶ Iterate over primer3 output as Bio.Emboss.Primer3.Record objects.
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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.