snps
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apriha
tools for reading, writing, merging, and remapping SNPs
The use of a metaclass to make Resource a singleton is a bit counter-intuitive. Particularly as users won't often interact with this class directly, and I've been caught out by...
Update the `dtype` of `rsid`, `chrom`, and `genotype` columns to be `pandas.StringDtype` as recommended [here](https://pandas.pydata.org/pandas-docs/stable/user_guide/text.html#text-data-types). Also require `pandas>1.0.0`.
Building on #107, consolidate several issues (e.g., `duplicate_rsid`, `discrepant_XY`) into one dataframe with the following columns / dtypes: Column | *pandas* dtype ------- | ---------------- `rsid` | `pd.StringDtype()` `chrom` |...
Duplicate SNPs can be reported for a particular locus in a file (e.g., two SNPs with the same position on the same chromosome, potentially with different genotypes). In one of...
Along the same lines as #108 has it been considered to use the Pandas nullable integer datatype (`pd.Int64Dtype()`) for `pos`? More details [here](https://pandas.pydata.org/pandas-docs/stable/user_guide/integer_na.html). We've seen a number of files that...
Merging snps from different samples and saving them as a multi-sample VCF. Hi, would that be possible? Thanks!
Ancestry and 23andme appear to have discrepant mapping of indel SNPs, causing them to be discarded by SNPs, and sometimes causing the program to fail. Indel SNPs positions where the...
Hi. Am trying out the codes. Understand that the raw files here mean genotype files from DTC companies. However, what I have is only vcf and gvcf files from in-house...
Create a new `Resolver` class to resolve SNP issues. Refactor `SNPs._assign_par_snps` to this class. Also, this class could be used to implement solutions to #13 and #19 .
Add ability to load mtDNA FASTA data (e.g., from [FTDNA](https://www.familytreedna.com)) and parse out mtDNA SNPs (see #9).