What's Changed

• move ag3/af1 to after species selection by @sanjaynagi in #44 . malariagen_data now requires authorisation - previously AnoPrimer loaded both ag3/af1 to begin with, this caused problems for some users who only had access to one of ag3,af1

Full Changelog: v1.0.1...v1.0.2

allows 2RL 3RL usage in gambiae_sl

Full Changelog: v1.0.0...v1.0.1

In this release, we rename the package to AnoPrimer, now that we can support An. funestus as well as An. gambiae.

What's Changed

• Change package name to AnoPrimer by @sanjaynagi in #43

Full Changelog: v0.6.9...v1.0.0

Minor change:

• Allele frequencies now rounded in plot_snp_frequencies() #42

• adds a function AgamPrimer.check_my_oligo() which uses gget to map an oligo sequence back to the AgamP3 genome, and then checks for variants in the Ag1000g/VObs #41

• adds support for anopheles funestus from af1000 project. #27

• workaround fix for num_expr bug in pd.query() #40

• updates to docs #36

• fix bug for when exactly 10 primers were designed #37

• Adds support for and pins to Primer3-py 2.0.0.
• Primer3-py 2.0.0 breaks AgamPrimer due to providing more diagnostic info.
• Previous versions did not pin primer3-py and so may not work from now on.

• Support for python 3.10, 3.11 from @alimanfoo in #30 to address #29.

In v0.5.12:

• designing cDNA primers that cover exon-exon junctions is now optional (PR #25)
• docstring for designPrimers() (PR #25)

In v0.5.11:

• in designPrimers(), if no primers can be found, a message and the primer3 run statistics are printed (PR #23)

• cDNA replaces qPCR throughout (when referring to cDNA gene expression style assays). qPCR didn't make sense, as gDNA primers can be used in qPCR.

• contig argument is removed from primary functions, instead users should supply a contig:position string as the target. for example 2L:28545767. For cDNA primers, target should be an AGAP identifier, from which the contig will be automatically determined.

• In the long notebook, there is now a single prepare_sequence function instead of two functions with an if else statement.

• I now use poetry to install/develop/publish on AgamPrimer and have specified dependencies properly, which was not configured before.
• Many small updates for the workshops
• github actions CI, which the notebooks with 3 different parameter sets
• gget_blat_genome() function which checks for specificity
• designPrimers() which runs whole workflow, for higher throughput.
• Notebooks are now names AgamPrimer-long.ipynb (normal, full version) and AgamPrimer-short.ipynb (one function version).