diff --git a/jass/models/worktable.py b/jass/models/worktable.py
index b21ce807627a6c6f62fbea988b286a4eb38e2998..32f147e7ae37d239a31066d33cfea236475758c0 100644
--- a/jass/models/worktable.py
+++ b/jass/models/worktable.py
@@ -525,6 +525,9 @@ def create_worktable_file(
if sum_stat_tab.shape[0] == 0:
print("No data available for region {0} to region {1}".format(binf, bsup))
+ file_progress = open(progress_path, "w")
+ file_progress.write(str(JASS_progress))
+ file_progress.close()
continue # skip region if no data are available
Nsnp_total = Nsnp_total + sum_stat_tab.shape[0]
@@ -668,6 +671,11 @@ def create_worktable_file(
print("{1} SNPs treated on {0} SNPs".format(Nsnp_jassed, Nsnp_total))
+ if (Nsnp_jassed == 0):
+ file_error = "ERROR_LOCAL_ANALYSIS_MSG.log"
+ msg_error = "There is no SNP in the selected region"
+ write_error_msg(project_hdf_path, file_error, msg_error)
+
RegionSubTable = read_hdf(project_hdf_path, "Regions")
pval_min = RegionSubTable["UNIVARIATE_MIN_PVAL"]
@@ -706,7 +714,10 @@ def create_worktable_file(
"summaryTable", summaryTable, format="table", data_columns=True
) # Summary Table (contigency table)
hdf_work.close()
-
+
+ if local_analysis:
+ add_annotation_region(init_file_path, project_hdf_path, chromosome, pos_Start, pos_End)
+
return Nchunk
@@ -1015,3 +1026,211 @@ def create_genome_full_csv(project_hdf_path, csv_file, chunk_size=50, Nchunk=35)
The_file_is_available = False
return The_file_is_available
+
+
+def extract_annotation_region(
+ init_file_path,
+ chromosome,
+ pos_Start,
+ pos_End
+):
+
+ """
+ Extract genes and exons from an initial data table
+ by specifying the selected region (chromosome and position start, end)
+
+ :param init_file_path: path to the initial data table
+ :type init_file_path: str
+ :param chromosome: Chromosome number selected for local analysis
+ :type chromosome: str
+ :param pos_Start: start of the position of the studied region (base point) for local analysis
+ :type pos_Start: str
+ :param pos_End: end of the position of the studied region (base point) for local analysis
+ :type pos_End: str
+
+ :return: execution status
+ :rtype: bool
+ :return: df_gene_exon
+ :rtype: dataframe of genes and exons
+ """
+
+ Genes_and_exons_are_available = False
+ df_gene_exon = None
+
+ condition = "Chr = {0} and start < {2} and end > {1}".format(chromosome, pos_Start, pos_End)
+
+ try:
+ df_gene = read_hdf(init_file_path,
+ "Gene",
+ columns=[
+ "Chr",
+ "GeneID",
+ "gene_label",
+ "start",
+ "end",
+ "direction",
+ "biotype"
+ ],
+ where=condition)
+
+ except KeyError:
+ print("WARNING: Gene annotation not available in inittable. \nUse inittable.add_gene_annotation to update inittable.hdf5")
+ return (Genes_and_exons_are_available, df_gene_exon)
+
+ Array_Gene = df_gene.to_numpy()
+ Dict_gene_label = {}
+ Dict_gene_start = {}
+ Dict_gene_end = {}
+ Dict_gene_direction = {}
+ Dict_gene_biotype = {}
+ for i in range(df_gene.shape[0]):
+ Dict_gene_label[Array_Gene[i][1]] = Array_Gene[i][2]
+ Dict_gene_start[Array_Gene[i][1]] = Array_Gene[i][3]
+ Dict_gene_end[Array_Gene[i][1]] = Array_Gene[i][4]
+ Dict_gene_direction[Array_Gene[i][1]] = Array_Gene[i][5]
+ Dict_gene_biotype[Array_Gene[i][1]] = Array_Gene[i][6]
+
+ try:
+ df_exon = read_hdf(init_file_path,
+ "Exon",
+ columns=[
+ "Chr",
+ "exon_label",
+ "GeneID",
+ "start",
+ "end",
+ "direction"
+ ],
+ where=condition)
+
+ except KeyError:
+ print("WARNING: Exon annotation not available in inittable. \nUse inittable.add_gene_annotation to update inittable.hdf5")
+ return (Genes_and_exons_are_available, df_gene_exon)
+
+ colonnes = ["GeneID",
+ "exon_label",
+ "exon_start",
+ "exon_end",
+ "gene_label",
+ "gene_start",
+ "gene_end",
+ "gene_direction",
+ "gene_biotype"]
+
+ Liste_gene = df_exon[colonnes[0]].values
+ gene_label = []
+ gene_start = []
+ gene_end = []
+ gene_direction = []
+ gene_biotype = []
+
+ for gene_id in Liste_gene:
+ gene_label.append(Dict_gene_label[gene_id])
+ gene_start.append(Dict_gene_start[gene_id])
+ gene_end.append(Dict_gene_end[gene_id])
+ gene_direction.append(Dict_gene_direction[gene_id])
+ gene_biotype.append(Dict_gene_biotype[gene_id])
+
+ df_gene_exon = DataFrame()
+ df_gene_exon[colonnes[0]] = df_exon[colonnes[0]]
+ df_gene_exon[colonnes[1]] = df_exon[colonnes[1]]
+ df_gene_exon[colonnes[2]] = df_exon["start"]
+ df_gene_exon[colonnes[3]] = df_exon["end"]
+ df_gene_exon[colonnes[4]] = gene_label
+ df_gene_exon[colonnes[5]] = gene_start
+ df_gene_exon[colonnes[6]] = gene_end
+ df_gene_exon[colonnes[7]] = gene_direction
+ df_gene_exon[colonnes[8]] = gene_biotype
+
+ Genes_and_exons_are_available = True
+ return (Genes_and_exons_are_available, df_gene_exon)
+
+
+def add_annotation_region(
+ init_file_path,
+ project_hdf_path,
+ chromosome,
+ pos_Start,
+ pos_End
+):
+
+ """
+ Add genes and exons to the worktable file from an initial data table
+ by specifying the selected region (chromosome and position start, end)
+
+ :param init_file_path: path to the initial data table
+ :type init_file_path: str
+ :param project_hdf_path: path to the worktable file that will be produced
+ :type project_hdf_path: str
+ :param chromosome: Chromosome number selected for local analysis
+ :type chromosome: str
+ :param pos_Start: start of the position of the studied region (base point) for local analysis
+ :type pos_Start: str
+ :param pos_End: end of the position of the studied region (base point) for local analysis
+ :type pos_End: str
+
+ :return: execution status
+ :rtype: bool
+ """
+ status, df_gene_exon = extract_annotation_region(init_file_path, chromosome, pos_Start, pos_End)
+
+ if status:
+ hdf_work = HDFStore(project_hdf_path)
+ hdf_work.put("gene_exon", df_gene_exon, format="table", data_columns=True)
+ hdf_work.close()
+ else:
+ file_error = "ERROR_GENE_EXON_MSG.log"
+ msg_error = "Gene and Exon annotations are not available. Run inittable.add_gene_annotation"
+ write_error_msg(project_hdf_path, file_error, msg_error)
+
+ return status
+
+
+def get_annotation_gene_exon_data(project_hdf_path: str,
+ init_file_path: str = None,
+ chromosome: str = None,
+ pos_Start: str = None,
+ pos_End: str = None):
+ """
+ Read and return the gene_exon dataframe from a worktable file
+ for a given chromosome and region for the Gene and Exon diagram
+
+ :param project_hdf_path: path to the worktable file
+ :type project_hdf_path: str
+
+ :return: The dataframe gene_exon corresponding to the genes and exons for a given chromosome and region, \
+ as a CSV formatted text
+ :rtype: str
+ """
+ if chromosome is None:
+ # Local analysis : the file project_hdf_path contains only useful information.
+ # No data filter is needed
+ df_gene_exon = read_hdf(project_hdf_path, "gene_exon")
+ else:
+ # Genome full analysis
+ df_gene_exon = extract_annotation_region(init_file_path,
+ chromosome,
+ pos_Start,
+ pos_End)
+
+ return df_gene_exon.to_csv()
+
+
+def write_error_msg(project_hdf_path, file_error, msg_error):
+ """
+ write_error_msg
+ writes an error message which is displayed in the web interface
+
+ :param project_hdf_path: path to the worktable file
+ :type project_hdf_path: str
+ :param file_error: name of the file where the message is stored
+ :type file_error: str
+ :param msg_error: error message text
+ :type msg_error: str
+
+ """
+ file_error_path = os.path.join(os.path.dirname(project_hdf_path),
+ file_error)
+ the_file = open(file_error_path, "w")
+ the_file.write(msg_error)
+ the_file.close()