xstreck1 / HPACED

Highest Peak Aligment for Capillary Electrophoresis Data

Highest Peak Aligment for Capillary Electrophoresis Data

Copyright (c) Dr. Adam Streck 2016
Distributed under the MIT open-source license

Usage

Used to align the timeline of datafiles based on the highest peak found after a certain timepoint.

The input files must contain two tab-separated columns of values.

1. The time of measurement.
2. The measurement value.

For example:

0.003333333333332291	0.0052799997
0.006666666666665625	0.00533
0.009999999999998958	0.00542
0.013333333333332292	0.00555
	...

Notes:

• The data are shifted w.r.t. a template file that must be provided by the user.
• The tool does not override the original data. The results are stored in the output location.
• Should the value be shifted before 0 time, it gets ignored.

Execution

Requires Python 2.7 or Python 3 or newer.

python HPACED.py [-h] [--timepoint TIMEPOINT] [--location LOCATION]
				 [--output OUTPUT] [--extension EXTENSION]
				 template


positional arguments:
  template              the name of the file found in the location based on
						which the files are aligned

optional arguments:
  -h, --help            show this help message and exit
  --timepoint TIMEPOINT
						ignores the data up till the timepoint (inclusive)
						(default: 0.0)
  --location LOCATION   a path in the filesystem to where the data are stores
						(default: .)
  --output OUTPUT       a path relative to the location where the results are
						to be stored (default: ./HPACED_OUT)
  --extension EXTENSION
						if set, only the files with the extension (e.g. .xy)
						are considered, if not, all files found in the
						location are tested (default: None)