Package: primer_designer
testspackageDesigns primers from a FASTA file using primers4clades websiteFree software: BSD licenseInstallationpip install primer_designerUsageIt will send a FASTA alignment toprimers4cladesin 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 alignmentstm (str):             temperaturemin_amplength (str):  minimum amplicon lengthmax_amplength (str):  maximum amplicon lengthgencode (str):        genetic code. See below for all available genetic codesclustype (str):       cluster distance metric:dna,protein.amptype (str):        substitution model used to estimate phylogenetic informationemail (str):          your email address so that primer4clades can send you email with detailed resultsExample:>>># The values shown are the default. Change them if needed.>>>fromprimer_designerimportPrimerDesigner>>>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.primers4cladeswill send you one email
for each alignment.
The genetic code table (variablegencode) 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 mitochondrialThe evolutionary substitution model can be any of the following (variableamptype):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+GDocumentationhttps://primer-designer.readthedocs.org/DevelopmentTo run the all tests run:toxRelease History0.2.0 (2015-10-27)After all FASTA alignments are processed, a report will be produced with the
codehop, relaxed and degen primers for the best amplicon (higher quality and
longer expeced sequence).0.1.1 (2015-10-23)Fixed bug that caused infinite loop if input FASTA alignment was incorrect and
primer4clades could not generate primers for.0.1.0 (2015-10-22)Add taxon name to description of FASTA seqs if given by user.0.0.1 (2015-10-22)Some refactoring and testing.Updated requirements.Added test rule to Makefile.Small fixes of style to code.Replaced name of changelog to history.0.0.0 (2015-10-06)First release on PyPI.