def show_dge_table(contrast, design, dataset, method):
print('Querying available DGE models ...')
from roger.persistence import db
import roger.persistence.dge
model = roger.persistence.dge.get_dge_model(db.session(), contrast, design, dataset, method)
print(model.result_table)
def remove_gmt(category_name):
print("Deleting gene set category '%s' ..." % category_name)
from roger.persistence import db
import roger.persistence.gse
roger.persistence.gse.delete_gmt(db.session(), category_name)
print("Done")
def get(self, study_name, design_name, contrast_name, dge_method_name):
session = db.session()
dge_table = get_dge_tbl(session, contrast_name, design_name, study_name, dge_method_name);
neg_log10_pvalue = -numpy.log10(dge_table.PValue)
log_fc = dge_table.LogFC
x_range = quantileRange(log_fc, symmetric=True)
y_range = [0, max(quantileRange(neg_log10_pvalue, symmetric=False))]
neg_log10_pvalue = -numpy.log10(dge_table.PValue)
log_fc = dge_table.LogFC
data = {'x': log_fc.tolist(),
'y': neg_log10_pvalue.tolist(),
'text': dge_table.GeneSymbol.tolist(),
'type': 'scatter',
'mode': 'markers'}
layout = {
"xaxis": {
"title": "logFC",
"range": x_range,
"showline": True,
},
"yaxis": {
"title": "-log10(PValue)",
"range": y_range,
"showline": True,
},
"width": 500,
"height": 500,
"title": "Volcano Plot"
}
return jsonify({'data': [data], 'layout': layout})
def remove_contrast(contrast_name, design_name, dataset_name):
print("Deleting contrast '%s' of design '%s' ..." % (contrast_name, design_name))
from roger.persistence import db
import roger.persistence.dge
roger.persistence.dge.remove_contrast(db.session(), contrast_name, design_name, dataset_name)
print("Done")
def list_gse_methods():
print('Querying available GSE methods ...')
from roger.persistence import db
import roger.persistence.gse
print(roger.persistence.gse.list_methods(db.session()))
print("Done")
def remove_dge_model(contrast, design, dataset, method):
print("Deleting DGE result from %s:%s:%s calculated with method %s" % (dataset, design, contrast, method))
from roger.persistence import db
from roger.persistence.dge import remove_dge_model
remove_dge_model(db.session(), contrast, design, dataset, method)
print("Done")
def remove_design(design_name, dataset_name):
print("Deleting design '%s' from data set '%s' ..." % (dataset_name, design_name))
from roger.persistence import db
import roger.persistence.dge
roger.persistence.dge.remove_design(db.session(), design_name, dataset_name)
print("Done")
def show_design(design, dataset):
print('Querying available DGE models ...')
from roger.persistence import db
from roger.persistence.dge import get_design
design = get_design(db.session(), design, dataset)
print(design.design_matrix)
def show_pheno_data(dataset):
print("Querying dataset '%s'..." % dataset)
from roger.persistence import db
from roger.persistence.dge import get_ds
ds = get_ds(db.session(), dataset)
print(ds.pheno_data)
def add_ds_ma(norm_exprs_file,
tax_id,
symbol_type,
pheno_file,
name,
normalization,
description,
xref):
name = get_or_guess_name(name, norm_exprs_file)
print("Adding microarray data set '%s' ..." % name)
from roger.persistence import db
import roger.logic.dge
import roger.persistence.dge
from roger.persistence.schema import MicroArrayDataSet
session = db.session()
print("Parsing and annotating data ...")
ds_prop = roger.logic.dge.create_ds(session,
MicroArrayDataSet,
norm_exprs_file,
tax_id,
symbol_type,
pheno_file,
name,
normalization,
description,
xref)
print("Persisting data set ...")
roger.persistence.dge.add_ds(session,
flask.current_app.config['ROGER_DATA_FOLDER'],
ds_prop)
print("Done - added data set with name '%s'" % name)
def remove_ds(name):
print("Deleting data set '%s' ..." % name)
from roger.persistence import db
import roger.persistence.dge
roger.persistence.dge.delete_ds(db.session(), name)
print("Done")
def show_contrast(contrast, design, dataset):
print('Querying available DGE models ...')
from roger.persistence import db
from roger.persistence.dge import get_contrast
contrast = get_contrast(db.session(), contrast, design, dataset)
print(contrast.contrast_matrix)
def export_contrast(contrast, design, dataset, out_file):
print("Exporting contrast matrix to '%s' ..." % out_file.name)
from roger.persistence import db
from roger.persistence.dge import get_contrast
contrast = get_contrast(db.session(), contrast, design, dataset)
contrast.contrast_matrix.to_csv(out_file, sep="\t")
print("Done")
def list_gse_tables(contrast, design, dataset, dge_method, gse_method):
print('Querying available GSE models ...')
from roger.persistence import db
import roger.logic.gse
print(
roger.logic.gse.list_gse_tables(db.session(), contrast, design,
dataset, dge_method, gse_method))
def export_design(design, dataset, out_file):
print("Saving design matrix to '%s' ..." % out_file.name)
from roger.persistence import db
from roger.persistence.dge import get_design
design = get_design(db.session(), design, dataset)
design.design_matrix.to_csv(out_file, sep="\t")
print("Done")
def export_pheno_data(dataset, out_file):
print("Saving pheno data to '%s' ..." % out_file.name)
from roger.persistence import db
from roger.persistence.dge import get_ds
ds = get_ds(db.session(), dataset)
ds.pheno_data.to_csv(out_file, sep="\t")
print("Done")
def list_species():
"""Used to retrieve a table of species whose gene annotation data has been imported into the database instance.
"""
print('Querying available species ...')
from roger.persistence import db
import roger.persistence.geneanno
print(roger.persistence.geneanno.list_species(db.session()))
def get(self, study_name, design_name, contrast_name, dge_method_name):
session = db.session()
dge_table = get_dge_tbl(session, contrast_name, design_name, study_name, dge_method_name)
return Response(dge_table.to_csv(index=False),
mimetype="text/csv",
headers={"Content-disposition": "attachment; filename=%s_%s_%s_%s.csv" %
(dge_method_name, study_name, design_name, contrast_name)})
def export_exprs(dataset, out_file):
print("Saving expression matrix to '%s' ..." % out_file.name)
from roger.persistence import db
from roger.persistence.dge import get_ds
import shutil
ds = get_ds(db.session(), dataset)
shutil.copy(ds.ExprsWC, out_file.name)
print("Done")
def remove_gene_anno(tax_id):
"""Used to delete imported gene annotation data from the database
"""
print("Deleted gene annotation for species %s" % tax_id)
from roger.persistence import db
import roger.persistence.geneanno
roger.persistence.geneanno.remove_species(db.session(), tax_id)
print("Done")
def export_dge_table(contrast, design, dataset, method, out_file):
print("Exporting DGE table to '%s' ..." % out_file.name)
from roger.persistence import db
from roger.logic.util.data import write_df
from roger.persistence.dge import get_dge_model
model = get_dge_model(db.session(), contrast, design, dataset, method)
write_df(model.result_table, out_file)
print("Done")
def add_gmt(category_name, gmt_file, tax_id):
print("Importing gene sets from GMT file '%s' ..." % gmt_file)
from roger.persistence import db
import roger.persistence.gse
roger.persistence.gse.add_gmt(
db.session(), flask.current_app.config['ROGER_DATA_FOLDER'],
category_name, gmt_file, tax_id)
print("Done")
def show_gse_table(contrast, design, dataset, dge_method, gse_method):
print('Querying GSE table ...')
from roger.persistence import db
import roger.logic.gse
result_table = roger.logic.gse.get_gse_table(db.session(), contrast,
design, dataset, dge_method,
gse_method)
print(result_table)
def remove_gse_table(contrast, design, dataset, dge_method, gse_method):
print("Deleting GSE result from %s:%s:%s:%s:%s" %
(dataset, design, contrast, dge_method, gse_method))
from roger.persistence import db
from roger.logic.gse import remove_gse_table
remove_gse_table(db.session(), contrast, design, dataset, dge_method,
gse_method)
print("Done")
def export_gse_table(contrast, design, dataset, dge_method, gse_method,
out_file):
print("Exporting GSE table to '%s' ..." % out_file.name)
from roger.persistence import db
from roger.logic.util.data import write_df
from roger.logic.gse import get_gse_table
result_table = get_gse_table(db.session(), contrast, design, dataset,
dge_method, gse_method)
write_df(result_table, out_file)
print("Done")
def __init_db_with_datasets():
init_test_db = True
if os.path.exists("%s/__data/with_datasets/database.db" %
__roger_main_dir):
init_test_db = False
app = __create_test_app(
"sqlite:///%s/__data/with_datasets/database.db" % __roger_main_dir,
"%s/__data/with_datasets/working_dir" % __roger_main_dir,
"%s/__data/with_datasets/cache" % __roger_main_dir)
if init_test_db is True:
print("Create test database 'with_dataset'")
with app.app_context():
db.create_all()
session = db.session()
add_species(session, human_dataset, human_tax_id)
add_species(session, mouse_dataset, mouse_tax_id)
add_ds(
session, app.config['ROGER_DATA_FOLDER'],
create_ds(session, MicroArrayDataSet,
"test_data/ds/ma-example-signals.gct", mouse_tax_id,
"affy_mouse430_2"))
add_design(
session,
"test_data/ds/ma-example-design.txt",
"ma-example-signals",
)
add_contrast(session, "test_data/ds/ma-example-contrast.txt",
"ma-example-design", "ma-example-signals")
add_ds(
session, app.config['ROGER_DATA_FOLDER'],
roger.logic.dge.create_ds(
session, RNASeqDataSet,
"test_data/ds/rnaseq-example-readCounts.gct", human_tax_id,
"entrezgene"))
add_design(session,
"test_data/ds/rnaseq-example-DesignMatrix.txt",
"rnaseq-example-readCounts",
sample_groups_file=
"test_data/ds/rnaseq-example-sampleGroups.txt",
sample_group_levels_file=
"test_data/ds/rnaseq-example-sampleGroupLevels.txt")
add_contrast(session,
"test_data/ds/rnaseq-example-ContrastMatrix.txt",
"rnaseq-example-DesignMatrix",
"rnaseq-example-readCounts")
return app
def run_dge_rnaseq(contrast, design, dataset):
print("Performing DGE algorithm ...")
from roger.persistence import db
import roger.logic.dge
roger.logic.dge.run_dge(db.session(),
flask.current_app.config['ROGER_DATA_FOLDER'],
contrast,
design,
dataset,
roger.logic.dge.EdgeRDGE())
print("Done")
def add_species(dataset, tax_id):
"""Used to import gene annotation data from Ensembl from a specific dataset / species
Example:
roger import-geneanno rnorvegicus_gene_ensembl 10116
"""
print("Importing gene annotation for species %s ..." % tax_id)
from roger.persistence import db
import roger.persistence.geneanno
roger.persistence.geneanno.add_species(db.session(), dataset, tax_id)
print("Done")
def add_contrast(contrast_matrix,
design,
dataset,
name,
description):
name = get_or_guess_name(name, contrast_matrix)
print("Adding contrast '%s' to data set '%s' ..." % (name, dataset))
from roger.persistence import db
import roger.persistence.dge
name = roger.persistence.dge.add_contrast(db.session(),
contrast_matrix,
design,
dataset,
name,
description)
print("Done - added contrast with name '%s'" % name)
def init_database():
"""Initializes the database with human gene annotation and default DGE / GSE methods
"""
print("Initializing database ...")
from roger.persistence import db
import roger.persistence.geneanno
import roger.logic.dge
print("Adding human gene annotation ...")
roger.persistence.geneanno.init(db)
# Add standard DGE methods
print("Adding standard DGE and GSE methods ...")
session = db.session()
roger.logic.dge.init_methods(session)
print("Done")
