v1.1.11

What's Changed

• Allow matching by seqhash (including negation with '^') by @matthuska in #115
• Add covsonar 1 precommit hook to run black and zimports, etc. by @matthuska in #116
• Reformat code using black + zimports. Fix file endings. Remove execute bit. by @matthuska in #117
• Check formatting with black on push or pull requests by @matthuska in #118
• Automatically update parent-child lineage info by @matthuska in #121
• Allow match query parameters to be read from a file by @matthuska in #123
• If match returns no rows, still output column names by @matthuska in #122

Full Changelog: v1.1.10...v1.1.11

v1.1.10

What's Changed

• Don't crash when filtering empty profile. Closes #112 by @matthuska in #113

Full Changelog: v1.1.9...v1.1.10

v1.1.9

What's Changed

• Avoid bug when deleting sequences which are identical to others by @matthuska in #103

Full Changelog: v1.1.7...v1.1.9

covSonar V1.1.7

covSonar release Sept. 2022 Updates

• fix construction of the parent-child relationship
• fix bugs (e.g., #74)
• minor changes
• update lineage file (to Sept 05, 2022)

covSonar V.1.1.6

covSonar release August 2022 Updates

• Change made in parent-child construction (Fix class problem)
• small change in Readme, changed in installation part.

covSonar v.1.1.5

No new feature was added, we fixed reported bugs *(e.g., Github issues and slack channel ), and made the covSonar more stable.

v1.1.3

covSoanr v.1.1.3

This release includes

Improvement

1.Readme.md

• All new features
• Q&A
• Update DB version and program version
• Meta table

2. Add function to update lineage information

Run update-lineage-info flag, it will download the latest version of lineages from https://github.com/cov-lineages/pango-designation/ and install in lib/lineage.all.tsv

# example command
path/to/covsonar/sonar.py update-lineage-info

3.Database

According to #21, We add the 'submission date' column to the genome table and also prot_viewand essence view *(submission_date TEXT). Then, now we can use the match command with the submission_date flag to define a condition. The submission date will always be included in the output result. for example;

python sonar.py match 
--db ../workdir_covsonar/mycacheV1/mydb.new.db  \
--date 2021-10-01   \
--submission_date ^2021-10-31 2021-10-20  

4.Improve error message

According to #22, We update the error message with the accession number.

5.Update test script

6.Parent-Child relationship

Now we can query all sublineages by using --with-sublineage tag along with match command.

# We want to get all sublineages of delta variant (B.1.617.2).
# This query will return result as ['B.1.617.2', 'AY.1', 'AY.2', ..., , 'AY.129', 'AY.130']
path/to/covsonar/sonar.py match -i S:N501Y --lineage  B.1.617.2 --with-sublineage --db mydb > out.csv

We use sublineage information from https://github.com/cov-lineages/pango-designation/ and create a custom script to automatically convert all information to precomputed lineage file (under lib/lineage.all.tsv).

New Features

1.Database upgrade assistant

In the upcoming future, if we have the new version of the database schema, we can just use this function to upgrade.

python sonar.py db-upgrade --db mydb.db 

This function will automatically update the database to the latest version.

# Example Output
Warning: Backup db file before upgrading, Press Enter to continue...

## press Enter
Current version: 3 Upgrade to: 4
Perform the Upgrade: file: mydb.db
Database now version: 4
Success: Database upgrade was successfully completed

2.Export DB to VCF file

covSonar can export accession records in a VCF format using the var2vcf command. The output from this feature is a single VCF file that combines all accessions. The output format is in .gz form.

# Export all accessions in the database.
path/to/covsonar/sonar.py var2vcf --db mydb -o merge.vcf
# Just like the option in the match command, we can use  --file, --acc and --date to enable specific accession export.
path/to/covsonar/sonar.py var2vcf --db mydb -f acc.10.txt -o merge.vcf
# To speed up the query, we can use --cpus tag to aid us.
path/to/covsonar/sonar.py var2vcf --db mydb --date 2021-08-01:2021-08-10 -o merge.vcf --cpus 20

# Another solution, we can use --betaV2 tag (x3-5 times faster), 
# The current version is under development, so if you found any bug please report it to us.
path/to/covsonar/sonar.py var2vcf --db mydb --date 2021-08-01:2021-08-10 -o merge.vcf --cpus 20 --betaV2

Bug fixes

• #16 #17 #23
• Minor bug fixes