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Refactor and reformat text data

Project description

### Installation:

$ pip install sliders

## text2table

### Description: Command-line tool to convert structured text data into CSV format. Currently includes built-in support for fastqc and samtools flagstat files. You can also provide a custom JSON file with instructions for parsing your text files. Text2table is a front-end tool for using the flextableparser python module.

### Usage:
# Convert a fastqc file into CSV format $ text2table –schema=fastqc fastqc.data # Write parsed CSV data to a file (1) $ text2table –schema=fastqc fastqc.data 2>&1 > fastqc.csv # Write parsed CSV data to a file (2) $ text2table –schema=fastqc –output_file=out.csv fastqc.data # Parse multiple input files $ text2table –schema=fastqc 1_fastqc.data 2_fastqc.data # Provide static values to be added as columns $ text2table –schema=fastqc –output_file=out.csv –static_values=series=test,sample=A fastqc.data # For debugging, only write log messages to the console $ text2table –schema=fastqc 1_fastqc.data 2_fastqc.data 2>&1 >/dev/null

## flextableparser

### Description: Python module for converting structred text data to CSV format.

### Usage:
>>> from sliders import flextableparser
>>> parser = flextableparser.FlexTableParser()
>>> parser.configure(json_file)
>>> parser.add_static_value(key, value)
>>> parser.parse_file(input_file)
>>> output = parser.parse_file(input_file)

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