diff --git a/rest/app.py b/rest/app.py index 66a124c..aef5def 100644 --- a/rest/app.py +++ b/rest/app.py @@ -15,6 +15,8 @@ limitations under the License. """ +from __future__ import print_function + from flask import Flask, request from flask_restful import Api, Resource diff --git a/scripts/parsing_models.py b/scripts/parsing_models.py index cc33fc7..2506cd7 100644 --- a/scripts/parsing_models.py +++ b/scripts/parsing_models.py @@ -17,7 +17,10 @@ limitations under the License. """ -import json, h5py +from __future__ import print_function + +import json +import h5py import numpy as np json_files = open('json_files.txt', 'r') @@ -36,52 +39,62 @@ uuid = objectdata['uuid'] # Create the HDF5 file - filename ="test_02.hdf5" + filename = "test_02.hdf5" f = h5py.File(filename, "a") - print(file_name[-1] + ' - ' + file_name[-3] + "\t" + objectdata['chrom'][0] + ' : ' + str(objectdata['chromStart'][0]) + ' - ' + str(objectdata['chromEnd'][0]) + " | " + str(int(objectdata['chromEnd'][0]-objectdata['chromStart'][0])) + " - " + str(len(models['models'][0]['data']))) + print( + file_name[-1] + ' - ' + file_name[-3] + "\t" + objectdata['chrom'][0] + + ' : ' + str(objectdata['chromStart'][0]) + ' - ' + str(objectdata['chromEnd'][0]) + + " | " + str(int(objectdata['chromEnd'][0]-objectdata['chromStart'][0])) + " - " + + str(len(models['models'][0]['data'])) + ) if str(resolution) in f: grp = f[str(resolution)] dset = grp['data'] - meta = grp['meta'] - mpgrp = meta['model_params'] - clustersgrp = meta['clusters'] + meta = grp['meta'] + mpgrp = meta['model_params'] + clustersgrp = meta['clusters'] centroidsgrp = meta['centroids'] else: # Create the initial dataset with minimum values - grp = f.create_group(str(resolution)) + grp = f.create_group(str(resolution)) meta = grp.create_group('meta') - mpgrp = meta.create_group('model_params') - clustersgrp = meta.create_group('clusters') + mpgrp = meta.create_group('model_params') + clustersgrp = meta.create_group('clusters') centroidsgrp = meta.create_group('centroids') - dset = grp.create_dataset('data', (1, 1000, 3), maxshape=(None, 1000, 3), dtype='int32', chunks=True, compression="gzip") + dset = grp.create_dataset( + 'data', (1, 1000, 3), maxshape=(None, 1000, 3), + dtype='int32', chunks=True, compression="gzip") - dset.attrs['title'] = objectdata['title'] + dset.attrs['title'] = objectdata['title'] dset.attrs['experimentType'] = objectdata['experimentType'] - dset.attrs['species'] = objectdata['species'] - dset.attrs['project'] = objectdata['project'] - dset.attrs['identifier'] = objectdata['identifier'] - dset.attrs['assembly'] = objectdata['assembly'] - dset.attrs['cellType'] = objectdata['cellType'] - dset.attrs['resolution'] = objectdata['resolution'] - dset.attrs['datatype'] = objectdata['datatype'] - dset.attrs['components'] = objectdata['components'] - dset.attrs['source'] = objectdata['source'] - dset.attrs['TADbit_meta'] = json.dumps(metadata) - dset.attrs['dependencies'] = json.dumps(objectdata['dependencies']) - dset.attrs['restraints'] = json.dumps(models['restraints']) + dset.attrs['species'] = objectdata['species'] + dset.attrs['project'] = objectdata['project'] + dset.attrs['identifier'] = objectdata['identifier'] + dset.attrs['assembly'] = objectdata['assembly'] + dset.attrs['cellType'] = objectdata['cellType'] + dset.attrs['resolution'] = objectdata['resolution'] + dset.attrs['datatype'] = objectdata['datatype'] + dset.attrs['components'] = objectdata['components'] + dset.attrs['source'] = objectdata['source'] + dset.attrs['TADbit_meta'] = json.dumps(metadata) + dset.attrs['dependencies'] = json.dumps(objectdata['dependencies']) + dset.attrs['restraints'] = json.dumps(models['restraints']) if 'hic_data' in models: - dset.attrs['hic_data'] = json.dumps(models['hic_data']) + dset.attrs['hic_data'] = json.dumps(models['hic_data']) clustergrps = clustersgrp.create_group(str(uuid)) - for c in range(len(clusters)): - clustersds = clustergrps.create_dataset(str(c), data=clusters[c], chunks=True, compression="gzip") + cluster_count = len(clusters) + for c in range(cluster_count): + clustersds = clustergrps.create_dataset( + str(c), data=clusters[c], chunks=True, compression="gzip") - centroidsds = centroidsgrp.create_dataset(str(uuid), data=models['centroids'], chunks=True, compression="gzip") + centroidsds = centroidsgrp.create_dataset( + str(uuid), data=models['centroids'], chunks=True, compression="gzip") current_size = len(dset) if current_size == 1: @@ -113,15 +126,15 @@ model_id += 1 - model_param_ds = mpgrp.create_dataset(str(uuid), data=model_param, chunks=True, compression="gzip") + model_param_ds = mpgrp.create_dataset( + str(uuid), data=model_param, chunks=True, compression="gzip") - model_param_ds.attrs['i'] = current_size - model_param_ds.attrs['j'] = current_size+(len(models['models'][0]['data'])/3) - model_param_ds.attrs['chromosome'] = objectdata['chrom'][0] - model_param_ds.attrs['start'] = int(objectdata['chromStart'][0]) - model_param_ds.attrs['end'] = int(objectdata['chromEnd'][0]) + model_param_ds.attrs['i'] = current_size + model_param_ds.attrs['j'] = current_size+(len(models['models'][0]['data'])/3) + model_param_ds.attrs['chromosome'] = objectdata['chrom'][0] + model_param_ds.attrs['start'] = int(objectdata['chromStart'][0]) + model_param_ds.attrs['end'] = int(objectdata['chromEnd'][0]) dset[current_size:current_size+(len(models['models'][0]['data'])/3), 0:1000, 0:3] += dnp f.close() -