old_readme

# thesis_tm
This will hold some of my notes, important links and snippets of codes for my thesis under prof Tobias Marschall

# VG related notes
* `vg snarls -r traversals_file_output graph.vg > snarls.pb`
The _snarls.pb_ file can then be turned to _json_ file with `vg view -R snarls.pb > snarls.json`
And the _traversals_file_output_ can be turned to _json_ file with `vg view -E traversals_file_output > traversals.json`

# Bandage related notes

# jq related notes
* If I wanted to selecte an object with a certain key and certain value. For example separating the ULTRABUBBLE from the snarls json file `jq 'select(.type | . and contains("ULTRABUBBLE"))' snarls.json` this will give back the objects that containe ultrabubbles.
* For _json_ files generated from the graphs, I have to read the files like this `jq '.[] | .[] | select(.id | . and contains("16534"))' graph.json`

# Python related notes
* Loading a json file with several dictionaries, I need to parse every line as one dictionary.
```python
with open("json_file.json", "r") as json_file:
	json_data = [json.loads(line) for line in json_file]
# for parsing the vg graph as json
with open("graph.vg.json", "r") as json_file:
	json_data = json.load(json_file)
# we'll get a dictionary with 2 keys, ['node', 'edge']
# each consisting of individual dictonaries
```
* For ipython to have auto reload, which means that we can just change a function in the imported file, and ipython will autmoaticaly reload the new functions in the file, no need to re-import it then.
```python
In [1]: %load_ext autoreload

In [2]: %autoreload 2

In [3]: from foo import some_function
```
# Vim related notes
* For searching and substituting, the following can be used to substitute foo with bar in only one line, to do it in all lines, we can add % before the s.
```
:s/foo/bar/g
```
* For Cut and paste, ctrl+v can be used for visual block, then d to cut (or y for copy) and p or P to paste.
* For mass indenting, use ctrl+v for visual block, the > character or < for un-indenting.
* For block commenting, also ctrl+v for visual block, the :s/^/# to insert the hash at the beginning of all the lines highlighted.