diff options
Diffstat (limited to 'wqflask/base/data_set/mrnaassaydataset.py')
| -rw-r--r-- | wqflask/base/data_set/mrnaassaydataset.py | 179 |
1 files changed, 0 insertions, 179 deletions
diff --git a/wqflask/base/data_set/mrnaassaydataset.py b/wqflask/base/data_set/mrnaassaydataset.py deleted file mode 100644 index 4eb998b5..00000000 --- a/wqflask/base/data_set/mrnaassaydataset.py +++ /dev/null @@ -1,179 +0,0 @@ -"MrnaAssayDataSet class ..." - -import codecs - - -from .dataset import DataSet -from .utils import geno_mrna_confidentiality -from wqflask.database import database_connection -from utility.tools import get_setting - -class MrnaAssayDataSet(DataSet): - ''' - An mRNA Assay is a quantitative assessment (assay) associated with an mRNA trait - - This used to be called ProbeSet, but that term only refers specifically to the Affymetrix - platform and is far too specific. - - ''' - - def setup(self): - # Fields in the database table - self.search_fields = ['Name', - 'Description', - 'Probe_Target_Description', - 'Symbol', - 'Alias', - 'GenbankId', - 'UniGeneId', - 'RefSeq_TranscriptId'] - - # Find out what display_fields is - self.display_fields = ['name', 'symbol', - 'description', 'probe_target_description', - 'chr', 'mb', - 'alias', 'geneid', - 'genbankid', 'unigeneid', - 'omim', 'refseq_transcriptid', - 'blatseq', 'targetseq', - 'chipid', 'comments', - 'strand_probe', 'strand_gene', - 'proteinid', 'uniprotid', - 'probe_set_target_region', - 'probe_set_specificity', - 'probe_set_blat_score', - 'probe_set_blat_mb_start', - 'probe_set_blat_mb_end', - 'probe_set_strand', - 'probe_set_note_by_rw', - 'flag'] - - # Fields displayed in the search results table header - self.header_fields = ['Index', - 'Record', - 'Symbol', - 'Description', - 'Location', - 'Mean', - 'Max LRS', - 'Max LRS Location', - 'Additive Effect'] - - # Todo: Obsolete or rename this field - self.type = 'ProbeSet' - self.query_for_group = """ -SELECT InbredSet.Name, InbredSet.Id, InbredSet.GeneticType, InbredSet.InbredSetCode -FROM InbredSet, ProbeSetFreeze, ProbeFreeze WHERE ProbeFreeze.InbredSetId = InbredSet.Id AND -ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND ProbeSetFreeze.Name = %s""" - - def check_confidentiality(self): - return geno_mrna_confidentiality(self) - - def get_trait_info(self, trait_list=None, species=''): - - # Note: setting trait_list to [] is probably not a great idea. - if not trait_list: - trait_list = [] - with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: - for this_trait in trait_list: - - if not this_trait.haveinfo: - this_trait.retrieveInfo(QTL=1) - - if not this_trait.symbol: - this_trait.symbol = "N/A" - - # XZ, 12/08/2008: description - # XZ, 06/05/2009: Rob asked to add probe target description - description_string = str( - str(this_trait.description).strip(codecs.BOM_UTF8), 'utf-8') - target_string = str( - str(this_trait.probe_target_description).strip(codecs.BOM_UTF8), 'utf-8') - - if len(description_string) > 1 and description_string != 'None': - description_display = description_string - else: - description_display = this_trait.symbol - - if (len(description_display) > 1 and description_display != 'N/A' - and len(target_string) > 1 and target_string != 'None'): - description_display = description_display + '; ' + target_string.strip() - - # Save it for the jinja2 template - this_trait.description_display = description_display - - if this_trait.chr and this_trait.mb: - this_trait.location_repr = 'Chr%s: %.6f' % ( - this_trait.chr, float(this_trait.mb)) - - # Get mean expression value - cursor.execute( - "SELECT ProbeSetXRef.mean FROM " - "ProbeSetXRef, ProbeSet WHERE " - "ProbeSetXRef.ProbeSetFreezeId = %s " - "AND ProbeSet.Id = ProbeSetXRef.ProbeSetId " - "AND ProbeSet.Name = %s", - (str(this_trait.dataset.id), this_trait.name,) - ) - result = cursor.fetchone() - - mean = result[0] if result else 0 - - if mean: - this_trait.mean = "%2.3f" % mean - - # LRS and its location - this_trait.LRS_score_repr = 'N/A' - this_trait.LRS_location_repr = 'N/A' - - # Max LRS and its Locus location - if this_trait.lrs and this_trait.locus: - cursor.execute( - "SELECT Geno.Chr, Geno.Mb FROM " - "Geno, Species WHERE " - "Species.Name = %s AND " - "Geno.Name = %s AND " - "Geno.SpeciesId = Species.Id", - (species, this_trait.locus,) - ) - if result := cursor.fetchone(): - lrs_chr, lrs_mb = result - this_trait.LRS_score_repr = '%3.1f' % this_trait.lrs - this_trait.LRS_location_repr = 'Chr%s: %.6f' % ( - lrs_chr, float(lrs_mb)) - - return trait_list - - def retrieve_sample_data(self, trait): - with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: - cursor.execute( - "SELECT Strain.Name, ProbeSetData.value, " - "ProbeSetSE.error, NStrain.count, " - "Strain.Name2 FROM (ProbeSetData, " - "ProbeSetFreeze, Strain, ProbeSet, " - "ProbeSetXRef) LEFT JOIN ProbeSetSE ON " - "(ProbeSetSE.DataId = ProbeSetData.Id AND " - "ProbeSetSE.StrainId = ProbeSetData.StrainId) " - "LEFT JOIN NStrain ON " - "(NStrain.DataId = ProbeSetData.Id AND " - "NStrain.StrainId = ProbeSetData.StrainId) " - "WHERE ProbeSet.Name = %s AND " - "ProbeSetXRef.ProbeSetId = ProbeSet.Id " - "AND ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id " - "AND ProbeSetFreeze.Name = %s AND " - "ProbeSetXRef.DataId = ProbeSetData.Id " - "AND ProbeSetData.StrainId = Strain.Id " - "ORDER BY Strain.Name", - (trait, self.name,) - ) - return cursor.fetchall() - - def retrieve_genes(self, column_name): - with database_connection(get_setting("SQL_URI")) as conn, conn.cursor() as cursor: - cursor.execute( - f"SELECT ProbeSet.Name, ProbeSet.{column_name} " - "FROM ProbeSet,ProbeSetXRef WHERE " - "ProbeSetXRef.ProbeSetFreezeId = %s " - "AND ProbeSetXRef.ProbeSetId=ProbeSet.Id", - (str(self.id),)) - return dict(cursor.fetchall()) |