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License: GNU General Public License v3.0
Key utils for sequence processing moved to a new home from bjorn
License: GNU General Public License v3.0
Need to generate latest metadata and send to SRA/Biosample process to upload
Changes in non-coding regions are currently moving most of Delta sequences to inspect folder. Mark suggests altering this such that
Will further consult with Mark and Karthik G. before taking out a branch against this issue.
Ideally this should be a passable property so the pipeline can be run in other places
Simply environment file to have only those dependencies required for bjorn_utils
Current date format gets changed by excel upon viewing, correct this so that excel knows what format the date should be in.
Currently the release workflow requires manually interacting with the GISAID
metadata tab. This issue and accompanying PR suggest these changes.
Will review these further before taking out new branch with Mark and Karthik G.
Add following potential filters that work in an automated way to flag sequences during release pipeline:
Metadata filters
Sequence filters
This will likely need to be sub-issued during implementation
Automated and combine the listed steps to reduce command overhead when generating output files
Example commands:
# inspect suspicious_mutations.csv
Combine msa/*_white.fa and *_inspect.fa
# Convert aligned to unaligned fasta
bash ~/code/bjorn/scripts/convert_to_unaigned_fasta.sh 2021-08-25_release_aligned_combined.fa > 2021-08-25_release_unaligned_combined.fa
# Convert multifastas to sindividual fasta preferably in a subfolder
bash ~/code/bjorn/scripts/multifasta_to_fasta.sh ../2021-08-25_release_unaligned_combined.fa
Need just 1 bam folder and 1 MSA folder - nothing else for the bjorn output
This currently sits in a notebook - need to update so we can generate the files that need to be uploaded and send it over to the ncbi_batch_push repo for action
Adjust output so that samples column is easier to read
Additionally, need a try: except clause since sometimes these data frames can be empty
Get data from these three sources and add to the metadata file
Need to automate the upload of files to these different sources
GISAID
Will review each of these portions with Mark and Karthik G. before taking out branch against them.
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