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Releases: iquasere/reCOGnizer

COG to KO conversion added

07 Sep 15:35
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  • 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

23 Jul 15:28
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1.2.5

update meta.yaml

blast info now outputed in protein report

15 Jul 12:15
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Joined protein2cog with blast info
CDD IDs to COGs now in cdd_aligned.txt

New parameters provide more information

03 Jun 14:41
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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

12 May 16:43
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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!

07 May 16:57
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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

05 May 11:11
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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:

Now outputs in TSV!

01 Apr 14:04
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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

27 Mar 16:09
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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

25 Mar 11:32
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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!