Distance matrix as output?

[jzrapp]

Hi @plpla,

I was wondering whether it would be possible to somehow retrieve the distance matrix as an output that your tools creates as a temporary file? Would be great to have for other analyses!

Thanks a lot,
Josephine

[nvaulin]

Hi, @jzrapp
I am not affiliated with the authors of CRISPRStudio, but the answer to your question is yes. Are you talking about the distance matrix returned by the table_to_distances(table, pairwise_distance_fn) function on lines 415-422? If so, see what could be done:

From the scikit-bio docs one can see that there is a to_file method of the DistanceMatrix object.

Thus simply edit the abovementioned function from that:

    def table_to_distances(table, pairwise_distance_fn):
        sample_ids = table.columns
        num_samples = len(sample_ids)
        data = zeros((num_samples, num_samples))
        for i, sample1_id in enumerate(sample_ids):
            for j, sample2_id in enumerate(sample_ids[:i]):
                data[i,j] = data[j,i] = pairwise_distance_fn(table, sample1_id, sample2_id)
        return DistanceMatrix(data, sample_ids)

To that:

    def table_to_distances(table, pairwise_distance_fn):
        sample_ids = table.columns
        num_samples = len(sample_ids)
        data = zeros((num_samples, num_samples))
        for i, sample1_id in enumerate(sample_ids):
            for j, sample2_id in enumerate(sample_ids[:i]):
                data[i,j] = data[j,i] = pairwise_distance_fn(table, sample1_id, sample2_id)
        dm = DistanceMatrix(data, sample_ids)
        dm.to_file(YOUR_FILENAME)
        return  dm

To make this edits i suppose it is easier to do it before installation:

git clone https://github.com/moineaulab/CRISPRStudio.git
cd CRISPRStudio
nano CRISPR_Studio_1.0.py # here edits the lines, you can use any text editor you prefer
./Install.sh

Maybe it's also worth to make this filename as an additional tool parameter for you. If you will be interested, i can comment on that.

Sincerely,
Nikita