Releases: iquasere/reCOGnizer
COG to KO conversion added
- Files are downloaded from StringDB
- COGs are converted to StringDB IDs and then to KOs
- All KOs for each COG are obtained in comma separated format
- Only retrieves KOs at the end of file protein.info, may be improved in the future
Bug fixed in RPS-BLAST handling
1.2.5 update meta.yaml
blast info now outputed in protein report
Joined protein2cog with blast info
CDD IDs to COGs now in cdd_aligned.txt
New parameters provide more information
Added two new parameters:
- --remove-spaces replaces spaces with underscores to keep the full IDs (BLAST disregards everything after a space)
- --output-sequences will output protein2cog with a new column, "Sequences", with the sequences of proteins inputed
Fully functional for bioconda
Even though reCOGnizer was already included in Bioconda, it has now been adapted to that new reality.
- Changed the header of the main script -> still can be run with python recognizer.py is coming from GitHub
- -rd option now fully functional (using the default with Bioconda may produce strange results)
- Added the version parameter -> now, you can track it!
Ready for Conda!
Made first modifications for including reCOGnizer into Conda.
- shifted Krona installation to Conda
- removed need for cdd2cog.pl script. Methods were created for implementing its functionality into main script
Introduced conversion of COG functions to EC numbers
Conversion of COG functions to EC numbers is based on some eggNOG tables that convert COG functions to STRING IDs and then to EC numbers. Many thanks go to SciLifeLab Bioinformatics LTS for composing all of this. Important files include:
- the script used for construction of the relational table of cog2ec
- the NOG.members.tsv table that allows conversion of COG functions to STRING IDs
- the eggnog4.protein_id_conversion.tsv table that allows conversion of STRING IDs to EC numbers
Now outputs in TSV!
Added parameter for writing tables in TSV format.
Also, cog_quantification now produces two tables, one for krona plotting, other for user interaction.
Different time for database construction
The code for construction of COG database from the SMP files has been improved.
- Latter stages of reCOGnizer are no longer dependent on reCOGnizer location and corresponding databases.
- Added parameters for specifying that database was built by reCOGnizer and for customizing directory of databases
Also reformulated the downloading of resources for cdd2cog.
- Migrated commands to new bash script, download_resources
- Removed the download at installation time of reCOGnizer
- Now, reCOGizer reacts at the absence of any of the files and runs the script to download everything again (might be overkill, but is safer)
reCOGnizer 1.1
Custom databases now allowed
Custom databases can be inputed
If multiple databases are inputed, multithreading can be used
Previous reCOGnizer databases can also now be inputed!