-
Notifications
You must be signed in to change notification settings - Fork 0
/
lookup.py
316 lines (220 loc) · 9.72 KB
/
lookup.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
from flask import Flask, Response, abort, redirect, url_for
from flask import render_template
from flask_sqlalchemy import SQLAlchemy
# Create the Flask application
app = Flask(__name__)
# Config the database
app.config['SQLALCHEMY_DATABASE_URI'] = 'sqlite:///SequenceDB.sqlite'
app.config['SQLALCHEMY_TRACK_MODIFICATIONS'] = False
# Start the database
db = SQLAlchemy(app)
# Get metadata for the table
db.Model.metadata.reflect(db.engine)
# Create the link table model
class Sequence ():
def __init__ (self, transcript_id, sequence):
self.Transcript_ID = transcript_id
self.Sequence = sequence
def __str__(self):
return str(self.Sequence)
# Create the link table model
class Genes (db.Model):
__tablename__ = 'Genes'
__table_args__ = { 'extend_existing': True }
Gene_ID = db.Column(db.Text, primary_key=True)
# Create the mRNA table model
class mRNA (db.Model):
__tablename__ = 'mRNA'
__table_args__ = { 'extend_existing': True }
Transcript_ID = db.Column(db.Text, primary_key=True)
# Create the protein table model
class Protein (db.Model):
__tablename__ = 'Protein'
__table_args__ = { 'extend_existing': True }
Transcript_ID = db.Column(db.Text, primary_key=True)
# Create the protein table model
class Orthologs (db.Model):
__tablename__ = 'Orthologs'
__table_args__ = { 'extend_existing': True }
Ortholog_ID = db.Column(db.Text, primary_key=True)
@app.route("/")
def index ():
# Render the index
return render_template("index.html")
@app.route('/gene/<gene_id>')
def gene (gene_id):
# Render the webpage
return render_template("gene.html", Gene_ID = gene_id)
@app.route('/mrna-lookup/<gene_id>')
def mrnaLookup(gene_id):
# Get the gene data from the database
gene_data = Genes.query.filter_by(Gene_ID=gene_id).first()
# Convert the transcript_ids into a list
transcript_IDs = gene_data.Transcript_IDs.split(', ')
# Check if anything was returned
if not gene_data:
return redirect(url_for('mrnaMissing', gene_id = gene_id))
# Create a list to store the transcript information
transcript_mRNAs = []
# Loop the transcripts
for transcript_ID in transcript_IDs:
# Get the transcript data from the database
mRNA_data = mRNA.query.filter_by(Transcript_ID=transcript_ID).first()
# Assign the new sequence object
transcript_mRNA = Sequence(mRNA_data.Transcript_ID, mRNA_data.Sequence.decode())
# Add the mRNA data to the list
transcript_mRNAs.append(transcript_mRNA)
# Check if anything was returned
if not transcript_mRNAs:
return redirect(url_for('mrnaMissing', Gene_ID = gene_id))
# Render the webpage
return render_template("mrna-lookup.html", Gene_ID = gene_id, mRNA_data_list = transcript_mRNAs)
@app.route("/gene-mRNAFasta/<gene_id>")
def geneMRNAFasta(gene_id):
# Get the gene data from the database
gene_data = Genes.query.filter_by(Gene_ID=gene_id).first()
# Convert the transcript_ids into a list
transcript_IDs = gene_data.Transcript_IDs.split(', ')
# Create a string to store the sequences
sequence = ''
# Loop the transcripts
for transcript_ID in transcript_IDs:
# Get the transcript data from the database
mRNA_data = mRNA.query.filter_by(Transcript_ID=transcript_ID).first()
# Assign the new sequence object
transcript_mRNA = Sequence(mRNA_data.Transcript_ID, mRNA_data.Sequence.decode())
# Add the sequence to the string
sequence += str(transcript_mRNA)
# Return the mRNA as a fasta file
return Response(sequence, mimetype="text/plain", headers={"Content-disposition":"attachment; filename=%s.fasta" % gene_id})
@app.route("/trans-mRNAFasta/<transcript_id>")
def transMRNAFasta(transcript_id):
# Get the mRNA from the database
mRNA_data = mRNA.query.filter_by(Transcript_ID=transcript_id).first()
# Return the mRNA as a fasta file
return Response(mRNA_data.Sequence, mimetype="text/plain", headers={"Content-disposition":"attachment; filename=%s.fasta" % transcript_id})
@app.route("/mrna-missing/<gene_id>")
def mrnaMissing (gene_id):
return render_template('not-found.html', Gene_ID = gene_id, data_type = 'mRNA')
@app.route('/protein-lookup/<gene_id>')
def proteinLookup(gene_id):
# Get the gene data from the database
gene_data = Genes.query.filter_by(Gene_ID=gene_id).first()
# Convert the transcript_ids into a list
transcript_IDs = gene_data.Transcript_IDs.split(', ')
# Check if anything was returned
if not gene_data:
return redirect(url_for('proteinMissing', gene_id = gene_id))
# Create a list to store the transcript information
transcript_AAs = []
# Loop the transcripts
for transcript_ID in transcript_IDs:
# Get the protein from the database
protein_data = Protein.query.filter_by(Transcript_ID=transcript_ID).first()
# Assign the new sequence object
transcript_AA = Sequence(protein_data.Transcript_ID, protein_data.Sequence.decode())
# Add the mRNA data to the list
transcript_AAs.append(transcript_AA)
# Check if anything was returned
if not transcript_AAs:
return redirect(url_for('proteinMissing', Gene_ID = gene_id))
# Render the webpage
return render_template("protein-lookup.html", Gene_ID = gene_id, protein_data_list = transcript_AAs)
@app.route("/gene-proteinFasta/<gene_id>")
def geneProteinFasta(gene_id):
# Get the gene data from the database
gene_data = Genes.query.filter_by(Gene_ID=gene_id).first()
# Convert the transcript_ids into a list
transcript_IDs = gene_data.Transcript_IDs.split(', ')
# Create a string to store the sequences
sequence = ''
# Loop the transcripts
for transcript_ID in transcript_IDs:
# Get the protein from the database
protein_data = Protein.query.filter_by(Transcript_ID=transcript_ID).first()
# Assign the new sequence object
transcript_AA = Sequence(protein_data.Transcript_ID, protein_data.Sequence.decode())
# Add the sequence to the string
sequence += str(transcript_AA)
# Return the protein as a fasta file
return Response(sequence, mimetype="text/plain", headers={"Content-disposition":"attachment; filename=%s.fasta" % gene_id})
@app.route("/trans-proteinFasta/<transcript_id>")
def transProteinFasta(transcript_id):
# Get the protein from the database
protein_data = Protein.query.filter_by(Transcript_ID=transcript_id).first()
# Return the protein as a fasta file
return Response(protein_data.Sequence, mimetype="text/plain", headers={"Content-disposition":"attachment; filename=%s.fasta" % transcript_id})
@app.route("/protein-missing/<gene_id>")
def proteinMissing (gene_id):
return render_template('not-found.html', Gene_ID = gene_id, data_type = 'Protein')
@app.route("/orthologs-lookup/<gene_id>")
def orthologLookup (gene_id):
# Get the gene data from the database
gene_data = Genes.query.filter_by(Gene_ID=gene_id).first()
# Check if anything was returned
if not gene_data or not gene_data.Ortholog_ID:
return redirect(url_for('orthoMissing', gene_id = gene_id))
# Get the ortholog data from the database
ortholog_data = Orthologs.query.filter_by(Ortholog_ID=gene_data.Ortholog_ID).first()
# Create a list to store the ortholog IDs
ortholog_gene_IDs = []
# Loop the transcript IDs using a split function
for ortholog_ID in ortholog_data.Transcript_IDs.split(', '):
# Assign the gene ID using the the transcript ID
ortholog_transcript_data = Genes.query.filter(Genes.Transcript_IDs.contains(ortholog_ID)).first()
# Assign the Gene ID
ortholog_gene_ID = ortholog_transcript_data.Gene_ID
# Check that ortholog isnt the query gene ID
if ortholog_gene_ID == gene_id:
continue
# Append the ID
ortholog_gene_IDs.append(ortholog_gene_ID)
# Sort the list
ortholog_gene_IDs.sort()
# Render the webpage
return render_template("orthologs-lookup.html", Gene_ID = gene_id, ortholog_id_list = ortholog_gene_IDs)
@app.route("/ortho-mRNAFasta/<gene_id>")
def orthoMRNAFasta (gene_id):
# Get the gene data from the database
gene_data = Genes.query.filter_by(Gene_ID=gene_id).first()
# Get the ortholog data from the database
ortholog_data = Orthologs.query.filter_by(Ortholog_ID=gene_data.Ortholog_ID).first()
# Conver the orthologs into a multi-line string
transcript_IDs = ortholog_data.Transcript_IDs.split(', ')
# Create a string to store the sequences
sequence = ''
# Loop the transcripts
for transcript_ID in transcript_IDs:
# Get the transcript data from the database
mRNA_data = mRNA.query.filter_by(Transcript_ID=transcript_ID).first()
# Assign the new sequence object
transcript_mRNA = Sequence(mRNA_data.Transcript_ID, mRNA_data.Sequence.decode())
# Add the sequence to the string
sequence += str(transcript_mRNA)
# Return the protein as a fasta file
return Response(sequence, mimetype="text/plain", headers={"Content-disposition":"attachment; filename=%s.fasta" % gene_id})
@app.route("/ortho-proteinFasta/<gene_id>")
def orthoProteinFasta (gene_id):
# Get the gene data from the database
gene_data = Genes.query.filter_by(Gene_ID=gene_id).first()
# Get the ortholog data from the database
ortholog_data = Orthologs.query.filter_by(Ortholog_ID=gene_data.Ortholog_ID).first()
# Conver the orthologs into a multi-line string
transcript_IDs = ortholog_data.Transcript_IDs.split(', ')
# Create a string to store the sequences
sequence = ''
# Loop the transcripts
for transcript_ID in transcript_IDs:
# Get the protein from the database
protein_data = Protein.query.filter_by(Transcript_ID=transcript_ID).first()
# Assign the new sequence object
transcript_AA = Sequence(protein_data.Transcript_ID, protein_data.Sequence.decode())
# Add the sequence to the string
sequence += str(transcript_AA)
# Return the protein as a fasta file
return Response(sequence, mimetype="text/plain", headers={"Content-disposition":"attachment; filename=%s.fasta" % gene_id})
@app.route("/ortho-missing/<gene_id>")
def orthoMissing (gene_id):
return render_template('not-found.html', Gene_ID = gene_id, data_type = 'Orthologs')
if __name__ == '__main__':
app.run(debug=True)