def process_upload(self, exp, *args, **kwargs):
"""
@param exp: Experiment
"""
self.clean_errors()
assay_df = pd.DataFrame.from_csv(self.es_matrix.get_file())
es = ExpressionSet(base_dir=exp.get_data_folder(),
base_filename="%s_annotation" % self.uuid)
pheno_df = pd.DataFrame.from_csv(self.pheno_matrix.get_file())
pheno_df.set_index(pheno_df.columns[0])
user_class_title = es.pheno_metadata["user_class_title"]
if user_class_title not in pheno_df.columns:
pheno_df[es.pheno_metadata["user_class_title"]] = ""
# if matrix is bad oriented, then do transposition
if self.es_matrix_ori == "GxS":
assay_df = assay_df.T
es.store_assay_data_frame(assay_df)
es.store_pheno_data_frame(pheno_df)
if self.working_unit:
es.working_unit = self.working_unit
self.set_out_var("expression_set", es)
exp.store_block(self)
self.do_action("success", exp)
def process_upload(self, exp, *args, **kwargs):
"""
@param exp: Experiment
"""
self.clean_errors()
assay_df = pd.DataFrame.from_csv(self.es_matrix.get_file())
es = ExpressionSet(base_dir=exp.get_data_folder(),
base_filename="%s_annotation" % self.uuid)
pheno_df = pd.DataFrame.from_csv(self.pheno_matrix.get_file())
pheno_df.set_index(pheno_df.columns[0])
user_class_title = es.pheno_metadata["user_class_title"]
if user_class_title not in pheno_df.columns:
pheno_df[es.pheno_metadata["user_class_title"]] = ""
es.store_assay_data_frame(assay_df)
es.store_pheno_data_frame(pheno_df)
if self.working_unit:
es.working_unit = self.working_unit
self.set_out_var("expression_set", es)
exp.store_block(self)
self.do_action("success", exp)
def process_upload(self, exp, *args, **kwargs):
"""
@param exp: Experiment
"""
# TODO: move to celery
self.clean_errors()
sep = getattr(self, "csv_sep", " ")
try:
if not self.pheno_matrix:
self.warnings.append(Exception("Phenotype is undefined"))
pheno_df = None
else:
pheno_df = self.pheno_matrix.get_as_data_frame(sep)
pheno_df.set_index(pheno_df.columns[0])
# TODO: solve somehow better: Here we add empty column with user class assignment
pheno_df[ExpressionSet(None, None).pheno_metadata["user_class_title"]] = ""
if self.m_rna_matrix is not None:
m_rna_assay_df = self.m_rna_matrix.get_as_data_frame(sep)
m_rna_es = ExpressionSet(base_dir=exp.get_data_folder(),
base_filename="%s_m_rna_es" % self.uuid)
m_rna_es.store_assay_data_frame(m_rna_assay_df)
m_rna_es.store_pheno_data_frame(pheno_df)
m_rna_es.working_unit = self.m_rna_unit
self.set_out_var("m_rna_es", m_rna_es)
# TODO: fetch GPL annotation if GPL id was provided
if self.mi_rna_matrix is not None:
mi_rna_assay_df = self.mi_rna_matrix.get_as_data_frame(sep)
mi_rna_es = ExpressionSet(base_dir=exp.get_data_folder(),
base_filename="%s_mi_rna_es" % self.uuid)
mi_rna_es.store_assay_data_frame(mi_rna_assay_df)
mi_rna_es.store_pheno_data_frame(pheno_df)
self.set_out_var("mi_rna_es", mi_rna_es)
if self.methyl_matrix is not None:
methyl_assay_df = self.methyl_matrix.get_as_data_frame(sep)
methyl_es = ExpressionSet(base_dir=exp.get_data_folder(),
base_filename="%s_methyl_es" % self.uuid)
methyl_es.store_assay_data_frame(methyl_assay_df)
methyl_es.store_pheno_data_frame(pheno_df)
self.set_out_var("methyl_es", methyl_es)
self.do_action("success", exp)
except Exception as e:
ex_type, ex, tb = sys.exc_info()
traceback.print_tb(tb)
self.do_action("error", exp, e)
def process_data_frame(exp, block, df, ori, platform, unit, data_type="m_rna"):
if settings.CELERY_DEBUG:
import sys
sys.path.append(
'/Migration/skola/phd/projects/miXGENE/mixgene_project/wrappers/pycharm-debug.egg'
)
import pydevd
pydevd.settrace('localhost',
port=6901,
stdoutToServer=True,
stderrToServer=True)
df.set_index(df.columns[0], inplace=True)
# if matrix is bad oriented, then do transposition
if ori == "GxS":
df = df.T
# df.columns = df.iloc[0]
# df = df.drop(df.index[0])
# if isinstance(df.columns[0][0], basestring):
gpl_file = None
if platform:
AllUpdated(exp.pk,
comment=u"Fetching platform %s" % platform,
silent=False,
mode=NotifyMode.INFO).send()
gpl_file = fetch_geo_gpl(exp, block, platform)
df, matched = convert_ids(gpl_file, df, data_type)
AllUpdated(exp.pk,
comment=u"Matched %s features for %s dataset" %
(matched, data_type),
silent=False,
mode=NotifyMode.INFO).send()
unit = 'RefSeq'
es = ExpressionSet(base_dir=exp.get_data_folder(),
base_filename="%s_%s_es" % (block.uuid, data_type))
es.working_unit = unit
es.store_assay_data_frame(df)
return es, df, gpl_file
def process_data_frame(exp, block, df, ori, platform, unit, data_type="m_rna"):
if settings.CELERY_DEBUG:
import sys
sys.path.append('/Migration/skola/phd/projects/miXGENE/mixgene_project/wrappers/pycharm-debug.egg')
import pydevd
pydevd.settrace('localhost', port=6901, stdoutToServer=True, stderrToServer=True)
df.set_index(df.columns[0], inplace=True)
# if matrix is bad oriented, then do transposition
if ori == "GxS":
df = df.T
# df.columns = df.iloc[0]
# df = df.drop(df.index[0])
# if isinstance(df.columns[0][0], basestring):
gpl_file = None
if platform:
AllUpdated(
exp.pk,
comment=u"Fetching platform %s" % platform,
silent=False,
mode=NotifyMode.INFO
).send()
gpl_file = fetch_geo_gpl(exp, block, platform)
df, matched = convert_ids(gpl_file, df, data_type)
AllUpdated(
exp.pk,
comment=u"Matched %s features for %s dataset" % (matched, data_type),
silent=False,
mode=NotifyMode.INFO
).send()
unit = 'RefSeq'
es = ExpressionSet(base_dir=exp.get_data_folder(),
base_filename="%s_%s_es" % (block.uuid, data_type))
es.working_unit = unit
es.store_assay_data_frame(df)
return es, df, gpl_file
def process_upload(self, exp, *args, **kwargs):
"""
@param exp: Experiment
"""
# TODO: move to celery
self.clean_errors()
sep = getattr(self, "csv_sep", " ")
try:
if not self.pheno_matrix:
self.warnings.append(Exception("Phenotype is undefined"))
pheno_df = None
else:
pheno_df = self.pheno_matrix.get_as_data_frame(sep)
pheno_df.set_index(pheno_df.columns[0])
# TODO: solve somehow better: Here we add empty column with user class assignment
pheno_df[ExpressionSet(
None, None).pheno_metadata["user_class_title"]] = ""
if self.m_rna_matrix is not None:
m_rna_assay_df = self.m_rna_matrix.get_as_data_frame(sep)
m_rna_es = ExpressionSet(base_dir=exp.get_data_folder(),
base_filename="%s_m_rna_es" %
self.uuid)
m_rna_es.store_assay_data_frame(m_rna_assay_df)
m_rna_es.store_pheno_data_frame(pheno_df)
m_rna_es.working_unit = self.m_rna_unit
self.set_out_var("m_rna_es", m_rna_es)
# TODO: fetch GPL annotation if GPL id was provided
if self.mi_rna_matrix is not None:
mi_rna_assay_df = self.mi_rna_matrix.get_as_data_frame(sep)
mi_rna_es = ExpressionSet(base_dir=exp.get_data_folder(),
base_filename="%s_mi_rna_es" %
self.uuid)
mi_rna_es.store_assay_data_frame(mi_rna_assay_df)
mi_rna_es.store_pheno_data_frame(pheno_df)
self.set_out_var("mi_rna_es", mi_rna_es)
if self.methyl_matrix is not None:
methyl_assay_df = self.methyl_matrix.get_as_data_frame(sep)
methyl_es = ExpressionSet(base_dir=exp.get_data_folder(),
base_filename="%s_methyl_es" %
self.uuid)
methyl_es.store_assay_data_frame(methyl_assay_df)
methyl_es.store_pheno_data_frame(pheno_df)
self.set_out_var("methyl_es", methyl_es)
self.do_action("success", exp)
except Exception as e:
ex_type, ex, tb = sys.exc_info()
traceback.print_tb(tb)
self.do_action("error", exp, e)
