PMAnalyzer is a command-line software pipeline that performs bacterial growth curve analysis for Multi-phenotype Assay Plates (MAPs). MAPs are 96-well micro-titer plates used to measure biomass formation through a spectrophotometer. Through the use of Python's SciPy and NumPy packages, PMAnalyzer performs curve-fitting in order to assess lag phase, growth rate, biomass yield, and growth level on each growth curve.
- Bash
- R
- Python 2.7.X+ or 3.X.X
- ggplot2
- ggthemes
- reshape2
- grid
- plyr
- SciPy
- NumPy
- Matplotlib (for graphs and figures)
- Pandas
The parsing scripts from PMAnalyzer are generated from the Molecular Devices Analyst GT multi-plate plate reader. Sample input files can be viewed in the
sample/data_csedlakii directory.
Filenames must be in the format of [sample]_[replicate]_[other].txt. For example
| Sample | Replicate | Filename |
|---|---|---|
| csedlakii | rep1 | csedlakii_rep1_2014Nov12.txt |
| csedlakii | rep2 | csedlakii_rep2_2014Nov12.txt |
| csedlakii | rep3 | csedlakii_rep3_2014Nov12.txt |
| ecoli | rep1 | ecoli_rep1_2014Nov15.txt |
| ecoli | rep2 | ecoli_rep2_2014Nov15.txt |
| ecoli | rep3 | ecoli_rep3_2014Nov15.txt |
sample and replicate names can have letters A-z, numbers 0-9, hyphens -, and periods . (periods for sample only).
(All output text files are tab-delimited)
- Various growth curves text files (raw, mean, median, logistic)
- Growth curve parameter text files (raw, logistic)
- Various growth curve figures
- Growth level heat-map
___ _ _
/ _ \/\/\ /_\ _ __ __ _| |_ _ _______ _ __
/ /_)/ \ //_\\| '_ \ / _` | | | | |_ / _ \ '__|
/ ___/ /\/\ \/ _ \ | | | (_| | | |_| |/ / __/ |
\/ \/ \/\_/ \_/_| |_|\__,_|_|\__, /___\___|_|
|___/
PMAnalyzer version 2.4
usage: runPM -c config_filename [Options]
OR
usage: runPM -i PM_data_directory -d output_directory -o output_name [Options]
Required
-c [config_filename] : Configuration file listing all parameters (this
takes precedence)
OR
-i [PM_data_directory] : PM data directory path to files
-d [output_directory] : Output directory (will create if non-existent)
-o [output_name] : Suffix appended to all output files
Optional
--clear : Clear out results directory of old files
--debug : Print out debug messages
-g : Flag to use experimental growth level calculation. Range: [1, 2]
-h, -?, --help : This help message
-m : Generate figures
-p [plate_filename] : Plate filepath
--python [file path] : Use specified Python executable [Default:
/usr/local/bin/python3]
-s [sample_filename] : Sample name and replicate file [used with -t 3 or 4]
-t [input_file_type] : Format number of PM plate format. Range: [1, 6] [Default: 1]
-v : Verbose output
Cuevas, D. A., & Edwards, R. A. (2017). PMAnalyzer: a new web interface for bacterial growth curve analysis. Bioinformatics, 33(12), 1905–1906. (doi: 10.1093/bioinformatics/btx084)