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Tidied up the code formatting
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@markmcdowall
markmcdowall committed Dec 18, 2017
1 parent 1768025 commit 7e03356
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Showing 2 changed files with 49 additions and 34 deletions.
2 changes: 2 additions & 0 deletions rest/app.py
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Expand Up @@ -15,6 +15,8 @@
limitations under the License.
"""

from __future__ import print_function

from flask import Flask, request
from flask_restful import Api, Resource

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81 changes: 47 additions & 34 deletions scripts/parsing_models.py
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Expand Up @@ -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')
Expand All @@ -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:
Expand Down Expand Up @@ -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()

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