primer_designer 0.2.0

Description:

primer designer 0.2.0

tests






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 = "[email protected]" # 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

Release History

0.2.0 (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.