agamprimer 0.4.5

A small package to store some functions for the the AgamPrimer notebook, to improve readability.

Primer Design in Anopheles gambiae s.l taking into account SNP variation in primer binding sites, using primer3-py and malariagen_data. Supports:

• genomic DNA primers
• quantitative PCR primers (cDNA, designed to span exon-exon junctions)
• probe design

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Release notes

• 0.4.0 - plot_primer_ag3_frequencies() now uses plotly to make an interactive plot, where one can hover over primer bases, which returns the exact frequency for each base.
• 0.3.4 - Fix bug in get_gDNA_sequence() and in plot_primer_locs()
• 0.3.3 - Introduced feature to enable a sample query (e.g subset to a specific species within a cohort)
• 0.3.2 - minor fix to remove printing of variable in plot_primer_ag3_frequencies()
• 0.3.1 - minor fix to bug introduced in 0.3.0 to plot_primer() function
• 0.3.0 - Support for probe design added, functions restructured to accommodate this