Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Genbank parser dev #61

Closed
wants to merge 3 commits into from
Closed

Genbank parser dev #61

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
6079108
added a notebook cleaning and parsing the covid pan genome as obtaine…
Bdegraaf1234 Apr 27, 2020
737c23d
Create README
Bdegraaf1234 Apr 27, 2020
26d0909
commit unsaved changes
Bdegraaf1234 Apr 27, 2020
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
15 changes: 15 additions & 0 deletions src/genbankParser/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
# serratus_genbankParser.Rmd

## Usage

not formatted as script yet

### Dependecies
Modules: R 4.0, BiocManager(devel), genbankr(devel), taxize, data.table, rlist, devtools, GenomicRanges, Biostrings, tidyverse
Files: cov0.gb, cov0.duplicates and cov0.id99.uc.

## Description

The genbankParser is designed to be run as a standalone script to generate a formatted and cleaned csv table of the covid pan-genome from genbank input. It deals with most hostTaxonId mapping errors, and attempts to infer these hostTaxonIds for duplicate and highly homologous entries by checking if clusters/duplicate all provide the same hostTaxonId and if so inferring it for those where none was prvided (in a new column).

Three meta-data files are required: the covid pan-genome from genbank [file](https://serratus-public.s3.amazonaws.com/seq/cov0/cov0.gb), the list of duplicates (generated here [file](https://github.com/ababaian/serratus/blob/master/notebook/200420_cov2_pangenome.ipynb) and a table containing homology information [file](https://serratus-public.s3.amazonaws.com/seq/cov2r/cov0.id99.uc) Filepaths have to be edited into the code as it stands