pyCSCS

Installation

Conda site

conda install -c askerdb pycscs

Examples

Download the small tests

wget https://raw.githubusercontent.com/askerdb/pyCSCS/master/tests/data/small_GNPS_buckettable.tsv
wget https://raw.githubusercontent.com/askerdb/pyCSCS/master/tests/data/small_GNPS_edges.tsv

Import the library and run the wrapper function that loads GNPS formatted formatted data

>>> import pyCSCS
>>> pyCSCS.cscs_from_files("small_GNPS_buckettable.tsv", "small_GNPS_edges.tsv")
          Sample1   Sample2   Sample3   Sample4   Sample5   Sample6
Sample1  0.000000  0.350203  1.000000  1.000000  1.000000  1.000000
Sample2  0.350203  0.000000  0.440548  1.000000  1.000000  1.000000
Sample3  1.000000  0.440548  0.000000  1.000000  1.000000  1.000000
Sample4  1.000000  1.000000  1.000000  0.000000  0.601044  1.000000
Sample5  1.000000  1.000000  1.000000  0.601044  0.000000  0.182195
Sample6  1.000000  1.000000  1.000000  1.000000  0.182195  0.000000

Other

To Download datasets from GNPS see the illustration in the q2-cscs user guide