trajectory_parser

Usage

Usage: parse_trajectory.js [options]

Options:
  -v, --verbose         Print verbose output                    [default: false]
  --vv, --very_verbose  Print extremely verbose output          [default: false]
  -f, --input           Load a trajectory file                        [required]
  -o, --output          Output transition probability matrix file               
  -t, --threshold       Set a threshold for basins                    [required]
  -h, --help            Show help                                               

Examples:
  parse_trajectory.js -t 10000 -f             generate the transition matrix
  trajectory.txt -o                           for trajectory.txt where basins
  transition_matrix.out                       of attraction take longer than
                                              10,000 steps to leave             

Missing required arguments: f, t

Example

Simple use case:

node parse_trajectory.js -v -f ../outLcollosomaFlux.txt -t 100

Returns something of the form:

_: 
  (empty array)
v:            true
verbose:      true
vv:           false
very_verbose: false
f:            ../outLcollosomaFlux.txt
input:        ../outLcollosomaFlux.txt
t:            100
threshold:    100
o:            
output:       
$0:           parse_trajectory.js
  parse_trajectory Starting to read the file +0ms
  parse_trajectory Lines read: 15906 +100ms
  parse_trajectory Number of basins: 919 +1ms
  parse_trajectory Number of unique basins: 16 +0ms
0:  ........(((((..(((((.((((...)))).)))))..)))...).).......
1:  ..((....(((((..(((((.((((...)))).)))))..)))...).))).....
2:  ........(((((..(((((.((((...)))).)))))..))).)...).......
3:  ..((..((..(((..(((((.((((...)))).)))))..))).).)..)).....
4:  ..((..(...(((..(((((.((((...)))).)))))..)))...)..)).....
5:  .........((((..(((((.((((...)))).)))))..))).)((....))...
6:  .......(..(((..(((((.((((...)))).)))))..))).)((....))...
7:  .....((...(((..(((((.((((...)))).)))))..)))..((....)))).
8:  ......((..(((..(((((.((((...)))).)))))..)))..((....)))).
9:  ..........(((..(((((.((((...)))).)))))..)))(.((....)))..
10: ..........(((..(((((.((((...)))).)))))..)))..((....))...
11: ......(...(((..(((((.((((...)))).)))))..))).)((....))...
12: ..........(((..(((((.((((...)))).)))))..)))(.((....)).).
13: ....((....(((..(((((.((((...)))).)))))..)))..((....)))).
14: ..((.(.(..(((..(((((.((((...)))).)))))..))).).)..)).....
15: ..((.(..(((((..(((((.((((...)))).)))))..))).)))..)).....
  parse_trajectory Building the transition matrix +0ms
  parse_trajectory Transition matrix complete +8ms

Contributing

1. Fork it ( https://github.com/evansenter/trajectory_parser/fork )
2. Create your feature branch (git checkout -b my-new-feature)
3. Commit your changes (git commit -am 'Add some feature')
4. Push to the branch (git push origin my-new-feature)
5. Create a new Pull Request