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Add support for indexing portein sequences #6

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sanjaysrikakulam wants to merge 1 commit into iqbal-lab-org:master from sanjaysrikakulam:v0.3.9

sanjaysrikakulam commented Jun 8, 2020

This pull request attempts to add support to index amino acid sequences

Changes to be made:

Update the config YAML files in the docs (https://bigsi.readme.io/docs/your-first-bigsi):
By default now the code expects to find the following key:value pair in the config YAML file.
sequence_type: nucleotides
or
sequence_type: aminoacids
I have updated the YAML files found in example-data/configs to adapt this.

The benefits of this PR are:

Building an index for protein sequences
Building an index directly from fasta, fastq, and a list of kmers in a .txt file


          Add support for indexing portein sequences

11c6992

Add features to index from fasta, fastq and extracted kmers in a txt file

iqbal-lab commented Jul 6, 2020

Apologies this has been ignored @sanjaysrikakulam.
I'll talk to @Zhicheng-Liu, @martinghunt and @leoisl today.

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