Sliders
Description:
Python package for refactoring and formatting text data.
Installation:
$ pip install sliders
Command-line Tools:
text2table
Description:
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
transpose
Description:
Transpose text file
Usage:
$ transpose -d="\s+" input_file.txt
$ transpose input_file.txt > transposed.txt
Modules
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)