Mergetable: The dataframe merge runner for CRISPResso2 out data.

Mergetable is the dataframe merge runner for CRISPResso2 out data. It designed to enable rapid and intuitive interpretation of genome editing experiments.

Install

Requirements

The script has been tested using the following softwares and their versions:

• python=3.10.11
• numpy=1.24.3
• pandas =2.0.2

If the dependency package is missing, the most convenient way is to install it directly with the command pip.

$ pip install numpy pandas

Clone the repository, install the dependencies and start the application. You must copy the Mergetable directory together.

git clone git@github.com:ligeng-k/Mergetable.git

cp -r Mergetable.linux.x86_64 you_installation_path/

By example (Mergetable.linux.x86_64):

$ Mergetable/Mergetable.linux.x86_64
├── Mergetable
└── Mergetable.pyarmor.rkey

1 directory, 2 files

Verify that Mergetable is installed using the command:

# Mergetable.linux.x86_64
$ export PATH=$PATH:you_installation_path/Mergetable.linux.x86_64
$ Mergetable -h
Mergetable -i <inputfile> -n <filename> -o <outputfile>

By example (Mergetable.windows.x86_64):

$ Mergetable/Mergetable.windows.x86_64
├── Mergetable.py
└── pyarmor_runtime_000000
    ├── __init__.py
    ├── __pycache__
    │   └── __init__.cpython-310.pyc
    └── pyarmor_runtime.pyd

3 directories, 4 files

Verify that Mergetable is installed using the command:

# Mergetable.linux.x86_64
$ python C:\Users\DZ\Desktop\Mergetable\Mergetable.py -h
Mergetable.py -i <inputfile> -n <filename> -o <outputfile>

Parameter List

-h : show a help message and exit.

-i : Sample list file.

-n : The name of the form you need to merge.

-o : Output folder to use for the analysis.

Getting Started

Run test

$ pip install numpy pandas

# samplelist.txt
$ cat test/samplelist.txt
1,2,3

Quantification_window_nucleotide_percentage_table.txt

	C	C	T	C	A
A	0	0.00110742	0	0.00110742	0.9944629
C	0.99778516	0.9944629	0.00110742	0.99335548	0
G	0	0.00221484	0	0	0.00110742
T	0	0	0.9944629	0.00110742	0
N	0	0	0	0	0
-	0.00221484	0.00221484	0.00442968	0.00442968	0.00442968

A very simple example that describes the code behaviour:

# Mergetable.windows.x86_64
$ cd test/
$ python C:\Users\DZ\Desktop\Mergetable\Mergetable.py -i samplelist.txt -n 
CRISPResso_quantification_of_editing_frequency -o out

$ python C:\Users\DZ\Desktop\Mergetable\Mergetable.py -i samplelist.txt -n Quantification_window_nucleotide_percentage_table -o out

# Mergetable.linux.x86_64
$ cd test/
$ Mergetable -i samplelist.txt -n CRISPResso_quantification_of_editing_frequency -o out
$ Mergetable -i samplelist.txt -n Quantification_window_nucleotide_percentage_table -o out

# test/
|-- CRISPResso_on_1
|   |-- CRISPResso_quantification_of_editing_frequency.txt
|   `-- Quantification_window_nucleotide_percentage_table.txt
|-- CRISPResso_on_2
|   |-- CRISPResso_quantification_of_editing_frequency.txt
|   `-- Quantification_window_nucleotide_percentage_table.txt
|-- CRISPResso_on_3
|   |-- CRISPResso_quantification_of_editing_frequency.txt
|   `-- Quantification_window_nucleotide_percentage_table.txt
|-- out
|   |-- CRISPResso_quantification_of_editing_frequency_Mergetable.csv
|   `-- Quantification_window_nucleotide_percentage_table_Mergetable.csv
`-- samplelist.txt

4 directories, 9 files

Run the example, and don't forget to watch it successfully!

=================================
    Table Merged Successfully!

                    .---- .
                .       、
                _·'__       ·
            . --(o) (o)---/#\
        .`@             /###\
        :         ,     #####
        `-..__.-'  _.- \###/
            `;_:       `"
                .'""""""`.
                /,         \\
            //           \\
            `-._________.-'
                __`.|.`__
            (_____|_____)

=================================

Output

Quantification_window_nucleotide_percentage_table_Mergetable.csv

Unnamed: 0	C	C.1	T	C.2	A	C.3
A	0	0.00110742	0	0.00110742	0.9944629	0
C	0.99778516	0.9944629	0.00110742	0.99335548	0	0.99335548
G	0	0.00221484	0	0	0.00110742	0.00110742
T	0	0	0.9944629	0.00110742	0	0.00110742
N	0	0	0	0	0	0
-	0.00221484	0.00221484	0.00442968	0.00442968	0.00442968	0.00442968
A	0	0.00110742	0	0.00110742	0.9944629	0
C	0.99778516	0.9944629	0.00110742	0.99335548	0	0.99335548
G	0	0.00221484	0	0	0.00110742	0.00110742
T	0	0	0.9944629	0.00110742	0	0.00110742
N	0	0	0	0	0	0
-	0.00221484	0.00221484	0.00442968	0.00442968	0.00442968	0.00442968
A	0	0.00110742	0	0.00110742	0.9944629	0
C	0.99778516	0.9944629	0.00110742	0.99335548	0	0.99335548
G	0	0.00221484	0	0	0.00110742	0.00110742
T	0	0	0.9944629	0.00110742	0	0.00110742
N	0	0	0	0	0	0
-	0.00221484	0.00221484	0.00442968	0.00442968	0.00442968	0.00442968

Manual

If you run into any problems, please contact me. https://github.com/ligeng-k/Mergetable