Added README

README.md

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+# countparticles
+
+[![DOI](https://zenodo.org/badge/DOI/.svg)](https://doi.org/)
+
+Report the number of particles in each class from a `run_data.star` file
+produced by RELION.
+
+A single-particle cryo-EM reconstruction comes from a set of particle images
+corresponding to projections of identical particles in different orientations.
+All datasets are heterogeneous, to various degrees, and data analysis involves
+classification of particle images. Knowing how many particles contributed to
+any given class is important to decide how to follow up after a classification
+job. This command-line tool reports a count of particles in each class in a
+`run_it???_data.star` file from a RELION Class2D or Class3D job. It can also
+optionally produce a bar plot of these particle counts.
+
+## Acknowledgments
+
+I would not have been able to put this tool together without the
+[`starfile`](https://github.com/alisterburt/starfile) library.
+
+## Installation
+
+```
+$ pip install countparticles
+```
+
+## Usage
+
+```
+$ countparticles --help
+Usage: countparticles [OPTIONS] <run_data.star>
+
+  Report the number of particles in each class from a run_data.star file
+  produced by RELION.
+
+Options:
+  -p, --plot         Optional. Display a bar plot of the particle counts. This
+                     is most helpful with only a few classes, e.g. for typical
+                     Class3D results (but not for typical Class2D results with
+                     many classes).
+
+  -o, --output TEXT  Optional. File name to save the barplot (recommended file
+                     formats: .png, .pdf, .svg or any format supported by
+                     matplotlib). This option has no effect without the
+                     -p/--plot option.
+
+  -h, --help         Show this message and exit.
+```