diff options
| -rw-r--r-- | wqflask/wqflask/heatmap/heatmap.py | 7 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/gemma_mapping.py | 9 | ||||
| -rw-r--r-- | wqflask/wqflask/marker_regression/run_mapping.py | 14 |
3 files changed, 18 insertions, 12 deletions
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py index 8d9c9e7f..8ef85d3c 100644 --- a/wqflask/wqflask/heatmap/heatmap.py +++ b/wqflask/wqflask/heatmap/heatmap.py @@ -33,9 +33,10 @@ class Heatmap: chrnames = [] self.species = species.TheSpecies(dataset=self.trait_list[0][1]) - for key in list(self.species.chromosomes(db_cursor).chromosomes.keys()): - chrnames.append([self.species.chromosomes.chromosomes[key].name, - self.species.chromosomes.chromosomes[key].mb_length]) + with database_connection() as conn, conn.cursor() as db_cursor: + for this_chr in self.species.chromosomes.chromosomes(db_cursor): + chrnames.append([self.species.chromosomes.chromosomes(db_cursor)[this_chr].name, + self.species.chromosomes.chromosomes(db_cursor)[this_chr].mb_length]) for trait_db in self.trait_list: diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index cc063d03..08a38527 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -11,6 +11,7 @@ from utility.tools import flat_files, assert_file from utility.tools import GEMMA_WRAPPER_COMMAND from utility.tools import TEMPDIR from utility.tools import WEBSERVER_MODE +from wqflask.database import database_connection from gn3.computations.gemma import generate_hash_of_string @@ -47,9 +48,11 @@ def run_gemma(this_trait, this_dataset, samples, vals, covariates, use_loco, gwa_output_filename = (f"{this_dataset.group.name}_GWA_" f"{generate_random_n_string(6)}") - this_chromosomes = this_dataset.species.chromosomes.chromosomes - this_chromosomes_name = [this_chromosomes[chromosome].name - for chromosome in this_chromosomes] + + this_chromosomes_name = [] + with database_connection() as conn, conn.cursor() as db_cursor: + for this_chr in this_dataset.species.chromosomes.chromosomes(db_cursor): + this_chromosomes_name.append(this_dataset.species.chromosomes.chromosomes(db_cursor)[this_chr].name) chr_list_string = ",".join(this_chromosomes_name) if covariates != "": diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py index b2f5af3b..8ca1faf5 100644 --- a/wqflask/wqflask/marker_regression/run_mapping.py +++ b/wqflask/wqflask/marker_regression/run_mapping.py @@ -30,6 +30,7 @@ from base import data_set from base import species from base import webqtlConfig from utility import webqtlUtil, helper_functions, hmac, Plot, Bunch, temp_data +from wqflask.database import database_connection from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_mapping, plink_mapping from wqflask.show_trait.SampleList import SampleList @@ -658,12 +659,13 @@ def geno_db_exists(this_dataset): def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results): chr_lengths = [] if mapping_scale == "physic": - for i, the_chr in enumerate(dataset.species.chromosomes.chromosomes): - this_chr = { - "chr": dataset.species.chromosomes.chromosomes[the_chr].name, - "size": str(dataset.species.chromosomes.chromosomes[the_chr].length) - } - chr_lengths.append(this_chr) + with database_connection() as conn, conn.cursor() as db_cursor: + for i, the_chr in enumerate(dataset.species.chromosomes.chromosomes(db_cursor)): + this_chr = { + "chr": dataset.species.chromosomes.chromosomes(db_cursor)[the_chr].name, + "size": str(dataset.species.chromosomes.chromosomes(db_cursor)[the_chr].length) + } + chr_lengths.append(this_chr) else: this_chr = 1 highest_pos = 0 |