Pycr documentation¶
A simple constrained-scope python utility to automate relative quantification of mRNA from thermocycler cycle threshold (ct) data. Takes as input raw ct values for target and reference genes from experiment and control conditions and returns as output the fold changes in gene expression using the Δ Δ ct method. Useful automation for repeatitive QPCR analyses for life science grad students and postdocs.
Installation:
$ python -m pip install git+https://github.com/pkmklong/pycr.git
Running pycr:
$ pycr -h
usage: pycr [-h] file_path control normalizer target
positional arguments:
file_path The path to ct data (csv) for relative RNA quantification
control The name of your control group
normalizer The name of your normalizing reference transcript
target The name of your target transcript
optional arguments:
-h, --help show this help message and exit
Input data dictionary:
{column: type description}
"group": str Names of comparison groups
user defined normalizing column: float ct values of normalizing reference transcript
user defined target column: float ct values of target transcript
Fold change:
Demo:
$ pycr ./data/demo_data_extended.csv control rpl19 egf1r
INFO:pycr: Loading table: ./data/demo_data_extended.csv
INFO:pycr: Calculating delta delta ct
INFO:pycr: Saving output table: data/demo_data_extended_processed.csv
| | group | rpl19 | egf1r | delta_ct | delta_delta_ct | fold_change |
|---:|:--------|--------:|--------:|-----------:|-----------------:|--------------:|
| 1 | control | 16.9 | 25.8 | 8.9 | 0.3335 | 0.793609 |
| 3 | control | 17.7 | 25.4 | 7.7 | -0.8665 | 1.82323 |
| 2 | control | 17.4 | 26 | 8.6 | 0.0335 | 0.977047 |
| 6 | control | 17.7 | 25.908 | 8.208 | -0.3585 | 1.28209 |
| 4 | control | 17.2 | 25.45 | 8.25 | -0.3165 | 1.24531 |
| 17 | trt_a | 17.4 | 24.786 | 7.386 | -1.1805 | 2.26655 |
| 20 | trt_b | 17.487 | 25.029 | 7.542 | -1.0245 | 2.03425 |
| 23 | trt_b | 17.3865 | 25.647 | 8.2605 | -0.306 | 1.23628 |
| 18 | trt_b | 17.9895 | 25.9498 | 7.96032 | -0.60618 | 1.52222 |
| 22 | trt_b | 17.9895 | 25.441 | 7.4515 | -1.115 | 2.16595 |
....
INFO:pycr: Saving output figure: data/demo_data_extended_processed.png
Note
Currently assumes perfect amplification efficiency and unpaired samples.
License¶
MIT License
Copyright (c) 2020 Patrick Long
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.