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Commit 4c4daeaa authored by Sean Leavey's avatar Sean Leavey

Update readme with examples

parent cc0a67af
......@@ -25,6 +25,72 @@ usage: fibrecnv <command> [<args>...]
```
As per the instructions, you can use the commands `list`, `convert` and `help`. To learn more about the first two commands, type `python3 -m fibrecnv help list` or `python3 -m fibrecnv help convert`. To just convert all of the fibre files in a directory, you would run `python3 -m fibrecnv convert /path/to/fibre/files`. There are optional parameters you can pass to `convert`, though, to turn on additional information output or to specify only a single identifier to convert - take a look at the help pages.
### Examples
Say you have fibre profiler data stored in the directory `/home/sean/fibres`. It contains three files:
- `10_02_2017 20170210_A0 Bottom Neck.xls`
- `10_02_2017 20170210_A0 Middle.xls`
- `10_02_2017 20170210_A0 Top Neck.xls`
- `11_02_2017 20170211_A1 Bottom Neck.xls`
- `11_02_2017 20170211_A1 Middle.xls`
- `11_02_2017 20170211_A1 Top Neck.xls`
To detect collections of profiler data, you would run the command:
```
$ python3 -m fibrecnv list /home/sean/fibres
```
This will output:
```
Found the following identifiers:
20170210_A0
20170211_A1
```
To convert them, execute the command:
```
$ python3 -m fibrecnv convert /home/sean/fibres
```
This will output nothing by default, but there will be new files called `20170210_A0.csv` and `20170211_A1.csv` in the same directory as the the input data. To view useful information output during the conversion process, add the `-v` flag to your command, after `fibrecnv`:
```
$ python3 -m fibrecnv -v convert /home/sean/fibres
```
This will output:
```
Using input directory to store output file
Extracting data for the following identifiers: 20170211_A1, 20170210_A0
Writing /home/sean/fibres/20170211_A1.csv
Top file data starts at row 1
Middle file data starts at row 1917
Bottom file data starts at row 2086
Output file contains 3522 rows
Writing /home/sean/fibres/20170210_A0.csv
Top file data starts at row 1
Middle file data starts at row 1917
Bottom file data starts at row 2086
Output file contains 3522 rows
```
You can enable _very_ verbose output by using the `-V` flag.
Note that if you convert the fibre files more than once, you will get an error message stating that output files already exist:
```
Using input directory to store output file
The following files already exist (specify -f to force overwrite): /home/sean/fibres/20170210_A0.csv, /home/sean/Workspace/fibres/20170211_A0.csv
```
You can force `fibrecnv` to overwrite existing output files using the `-f` flag:
```
$ python3 -m fibrecnv -f convert /home/sean/fibres
```
You can also combine the useful information output and forcing of output file overwriting:
```
$ python3 -m fibrecnv -vf convert /home/sean/fibres
```
If you wish to store the output files in a different directory from the input files, specify the output path with the `-o` setting after the input directory:
```
$ python3 -m fibrecnv -v convert /home/sean/fibres -o /home/sean/fibres/output
```
If this directory does not exist, you will get an error:
```
Output directory is not writeable
```
To fix this, ensure the output directory exists and can be written to by the current user.
## Credits
Sean Leavey
sean.leavey@glasgow.ac.uk
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