Primer designer
tests | |
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package |
Designs primers from a FASTA file using primers4clades website
- Free software: BSD license
Installation
pip install primer_designer
Usage
It will send a FASTA alignment to primers4clades in order to design degenerate primers. Input data needed is an alignment in FASTA format containing at least 4 sequences. It is recommended that the beginning of each FASTA sequence description contains the taxon name between square brackets.
Parameters:
- folder (str): path of folder containing the FASTA file alignments
- tm (str): temperature
- min_amplength (str): minimum amplicon length
- max_amplength (str): maximum amplicon length
- gencode (str): genetic code. See below for all available genetic codes
- clustype (str): cluster distance metric:
dna
,protein
. - amptype (str): substitution model used to estimate phylogenetic information
- email (str): your email address so that primer4clades can send you email with detailed results
Example:
>>> # The values shown are the default. Change them if needed.
>>> from primer_designer import PrimerDesigner
>>> pd = PrimerDesigner()
>>> pd.folder = "alignments" # folder containing the FASTA file alignments
>>> pd.tm = "55" # annealing temperature
>>> pd.min_amplength = "250" # minimum amplicon length
>>> pd.max_amplength = "500" # maximum amplicon length
>>> pd.gencode = "universal" # see below for all available genetic codes
>>> pd.mode = "primers"
>>> pd.clustype = "dna"
>>> pd.amptype = "dna_GTRG" # substitution model used to estimate phylogenetic information
>>> pd.email = "youremail@email.com" # primer4clades will send you an email with very detailed results
>>> pd.design_primers()
The best primer pairs will be printed to your screen. Detailed results will
be saved as HTML files in your alignments folder. But it is recommended if
you also get the results by email. primers4clades will send you one email
for each alignment.
The genetic code table (variable gencode
) can be any of the following:
-
universal
for standard -
2
for vertebrate mitochondrial -
3
for yeast mitochondrial -
4
for mold and protozoa mitochondrial -
5
for invertebrate mitochondrial -
6
for ciliate -
9
for echinoderm and flatworm -
10
for euplotid nuclear -
11
for bacterial and plastid -
12
for alternative yeast nuclear -
13
for ascidian mitochondrial -
14
for flatworm mitochondrial -
15
for Blepharisma nuclear -
16
for Chlorophycean mitochondrial -
21
for Trematode mitochondrial -
22
for Scenedesmus obliquus mitochondrial -
23
for Thraustochytrium mitochondrial
The evolutionary substitution model can be any of the following (variable amptype
):
-
protein_WAGG
for protein WAG+G -
protein_JTTG
for protein JTT+G -
protein_Blosum62G
for protein Blosum62+G -
protein_VTG
for protein VT+G -
protein_DayhoffG
for protein Dayhoff+G -
protein_MtREVG
for protein MtREV+G -
dna_HKYG
for dna HKY+G -
dna_GTRG
for dna GTR+G -
dna_K80G
for dna K80+G -
dna_TrNG
for dna TrN+G -
dna_JC69G
for dna JC69+G
Documentation
https://primer-designer.readthedocs.org/
Development
To run the all tests run:
tox