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Designs primers from a FASTA file using primers4clades website
- Free software: BSD license
pip install primer_designer
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:
universalfor standard2for vertebrate mitochondrial3for yeast mitochondrial4for mold and protozoa mitochondrial5for invertebrate mitochondrial6for ciliate9for echinoderm and flatworm10for euplotid nuclear11for bacterial and plastid12for alternative yeast nuclear13for ascidian mitochondrial14for flatworm mitochondrial15for Blepharisma nuclear16for Chlorophycean mitochondrial21for Trematode mitochondrial22for Scenedesmus obliquus mitochondrial23for Thraustochytrium mitochondrial
The evolutionary substitution model can be any of the following (variable amptype):
protein_WAGGfor protein WAG+Gprotein_JTTGfor protein JTT+Gprotein_Blosum62Gfor protein Blosum62+Gprotein_VTGfor protein VT+Gprotein_DayhoffGfor protein Dayhoff+Gprotein_MtREVGfor protein MtREV+Gdna_HKYGfor dna HKY+Gdna_GTRGfor dna GTR+Gdna_K80Gfor dna K80+Gdna_TrNGfor dna TrN+Gdna_JC69Gfor dna JC69+G
https://primer-designer.readthedocs.org/
To run the all tests run:
tox