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Change Logs

Change Logs#

Version 4.0#

4.0.0#

Features

  1. CAZyme substrate prediction based on dbCAN-sub;

  2. CGC substrate prediction based on dbCAN-PUL searching and dbCAN-sub majority voting. For CGC substrate prediction, please see our dbCAN-seq update paper for details. With these new functions (esp. the dbCAN-sub search), run_dbcan 4.0 is now slower to get the result back to you. Please be patient!

  3. See #127 for some explanation of different output files for substrate predictions.

BugFix

  • Please split your files if your input contains > 1 million proteins.

Regular Updates

  • All the databases are updated.

Version 3.0#

3.0.7#

BugFix

  • Fix the bug in cgc_parser.py.

Regular Updates

  • hmmdb, cazydb, tf-1, tf-2, stp and tcdb are updated.

3.0.6#

Feature

  • We now create the bioconda version. To old users, please run conda install dbcan -c bioconda for update from now on. To new users, please follow the installation instruction below.

    conda create -n run_dbcan python=3.8 dbcan -c conda-forge -c bioconda
conda activate run_dbcan

Updates

  • Rename the code hmmscan-parser.py to hmmscan_parser.py.

3.0.5#

Feature

  • Please use pip install dbcan==3.0.5 for updates.

BugFix

  1. Fixed the bug in signalP;

  2. Fixed the cgc and run_dbcan small bugs.

3.0.4#

Updates

  • Please use pip install dbcan==3.0.4 for update.

BugFix

  1. Fixed the eCAMI tool problem.

  2. If you download gff file from NCBI, please check the last column, replace Name with ID, and ID with Name.

3.0.2#

Feature

  1. Added the eCAMI tool and removed Hotpep.

  2. Changed the format of cgc.out to make it easy to read.

  3. Re-arranged the code. The command line is run_dbcan now without the suffix .py.

  4. The database files under db folder is now hosted through Git-LFS. To download the complete db files, please use the command git lfs pull (Note: To use git lfs, please check the installation guide at https://git-lfs.github.com/).

  5. Dockerfile is updated and we simplify the installation step.

BugFix

  • Fixed -t all which will cause the program to generate empty files.

Regular Updates

  • Updated CAZy db for Diamond and HMMER DB for HMMER.

Version 2.0#

2.0.11#

Feature

  1. Add ec number prediction to Hotpep result.

  2. dbCAN2 Hotpep PPR patterns updated to most recent release of CAZyDB (2019). Also missing group EC# files for families added in.

  3. Revising the output name file in Hotpep as random number, to make the program more robust for paralleing running.

  4. Prioritizing the CAZyme prediction over TF/TC/STP prediction when preparing gff input file for CGC-Finder.

  5. Rewrite the installation steps. Recommend user to use customized virtual environment (use certain Python version).

BugFix

  1. Fix the duplicate ACC of tf-2.hmm to make it compatiable for the newest hmmer(3.3). Delete version limitatino to hmmer.

  2. Fix the prodigal predicted gff file end with ";" problem.

2.0.6 (02/17/2020)#

Feature

  1. Please use pip install run-dbcan==2.0.6 for update.

  2. We forgo FragGeneScan because this program does not work now. We use Prodigal instead. So, you don’t need to use conda install fraggenescan now.

  3. We add extra information EC number to the last columns of Hotpep output to make it consistent with previous Hotpep result.

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