Cuterle v2.1.0

Update v2.1.0

This is the v2.1.0 stable release of Cuterle, a bioinformatic tool which return an output file (extracted_domain.fasta) containing every domain annotated by InterProScan (~.tsv file) via Pfam or SMART analysis from the list of protein (~.fasta file) submitted.

New features

• Graphical output: now
• Everytime Cuterle runs new analysis a new "YYYY/MM/DD_Analysis_number_X" folder is created

Minor update

General

• Log file is used to trace the file name's counter
• Minor updates

Manual and Assisted mode

• MInor updates

Bug fixes

Nothing to report (yet).

Install the requirements in your env

# Install requirements
pip install -r requirements.txt

Usage

Manual mode (the powerful one):

# Run main.py -h to see every possible options
python3 main.py [everything you decide to do]

Assisted mode:

# Run main.py and follow the instructions printed on screen
python3 main.py

Graphical mode:

# Run main_gui.py to have a graphical view of Cuterle
python3 main_gui.py

Cuterle v2.0.0

Update v2.0.0

This is the v2.0.0 stable release of Cuterle, a bioinformatic tool which return an output file (extracted_domain.fasta) containing every domain annotated by InterProScan (~.tsv file) via Pfam or SMART analysis from the list of protein (~.fasta file) submitted.

New features

• Analysis selection update: now Cuterle chooses for every sequence the analysis with more result
• New graphical mode, just run 'main_gui.py'
• All biggest operation became functions

Minor update

General

• Code and code comments reorganized and rewritten

Manual and Assisted mode

• MInor updates

Bug fixes

Nothing to report (yet).

Install the requirements in your env

# Install requirements
pip install -r requirements.txt

Usage

Manual mode (the powerful one):

# Run main.py -h to see every possible options
python3 main.py [everything you decide to do]

Assisted mode:

# Run main.py and follow the instructions printed on screen
python3 main.py

Graphical mode:

# Run main_gui.py to have a graphical view of Cuterle
python3 main_gui.py

Cuterle v1.3.0

Update v1.3.0

This is the v1.3.0 stable release of Cuterle, a bioinformatic tool which return an output file (extracted_domain.fasta) containing every domain annotated by InterProScan (~.tsv file) via Pfam or SMART analysis from the list of protein (~.fasta file) submitted.

New features

• Argument command line updated: now is possible extracting only selected domains by InterPro accession (e.g. IPR002035)

Minor update

General

• Code and code comments reorganized

Manual and Assisted mode

• Every domain has a default color which is the same for all the proteins

Assisted mode only

• Improved the graphics
• Improved the texts

Manual mode only

• Minor updates

Bug fixes

Nothing to report (yet).

Installation

# Install requirements
pip install -r requirements.txt

# Run Cuterle and follow the monitor-printed istruction
python3 main.py

Cuterle v1.2.0

Update v1.2.0

This is the v1.2.0 stable release of Cuterle, a bioinformatic tool which return an output file (extracted_domain.fasta) containing every domain annotated by InterProScan (~.tsv file) via Pfam or SMART analysis from the list of protein (~.fasta file) submitted.

New features

• Argument command line added : see the details on readme.md for the complete review

Minor update

General

• Code comments reorganized
• The drawer function now has its private file -> drawer.py
• The extracted domains' list now is more human readable

Manual and Assisted mode

• The list of domains' name extracted can be saved in an ~.csv file

Assisted mode only

• Improved the graphics
• Improved the texts
• List of files in the folders limited to 6

Manual mode only

• Possibility of choice for the name's format of sequences in fasta output

Bug fixes

Nothing to report (yet).

Installation

# Install requirements
pip install -r requirements.txt

# Run Cuterle and follow the monitor-printed istruction
python3 main.py

Cuterle v1.1.0

Update v1.1.0

This is the v1.1.0 stable release of Cuterle, a bioinformatic tool which return an output file (extracted_domain.fasta) containing every domain annotated by InterProScan (~.tsv file) via Pfam or SMART analysis from the list of protein (~.fasta file) submitted.

New features

• Graphical output [optional] reporting a schematic visualization of the protein and its domains
• Improved quality for the extraction method (now the program check how much results are given by Pfam and SMART, choosing the bigger one)
• The analysis used to extract the domain (Pfam or SMAR) is now graphically reported
• Summary table (first column Domain name, second column Domain's number found) is now graphically printed

Minor update

• Comments reorganized
• Requirements updated
• Added two file ( ~.tsv and ~.fasta) as example to test the program

Bug fixes

Nothing to report (yet).

Installation

# Install requirements
pip install -r requirements.txt

# Run Cuterle and follow the monitor-printed istruction
python3 main.py

Cuterle v1.0.0 - First stable release

This is the very first stable version of Cuterle, a bioinformatic tool which return an output file (extracted_domain.fasta) containing every domain annotated by InterProScan (~.tsv file) via Pfam from the list of protein (~.fasta file) submitted.

Installation

# Install requirements
pip install -r requirements.txt

# Run Cuterle and follow the monitor-printed istruction
python3 main.py