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-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py177
1 files changed, 100 insertions, 77 deletions
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index 2c99d1fc..96a91452 100644
--- a/wqflask/wqflask/marker_regression/gemma_mapping.py
+++ b/wqflask/wqflask/marker_regression/gemma_mapping.py
@@ -1,4 +1,4 @@
-import os, math
+import os, math, string, random, json
from base import webqtlConfig
from base.trait import GeneralTrait
@@ -20,7 +20,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
this_chromosomes = this_dataset.species.chromosomes.chromosomes
chr_list_string = ""
- for i in range(this_chromosomes):
+ for i in range(len(this_chromosomes)):
if i < (len(this_chromosomes) - 1):
chr_list_string += this_chromosomes[i+1].name + ","
else:
@@ -28,97 +28,77 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco):
if covariates != "":
gen_covariates_file(this_dataset, covariates)
- if method == "gemma":
- #gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -c %s/%s_covariates.txt -o %s_output' % (flat_files('mapping'),
- gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 1 -maf 0.1 -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'),
- this_dataset.group.name,
- flat_files('mapping'),
- this_dataset.group.name,
- flat_files('mapping'),
- this_dataset.group.name,
- webqtlConfig.GENERATED_IMAGE_DIR,
- this_dataset.group.name)
- # use GEMMA_RUN in the next one, create a unique temp file
+
+ if method == "gemma":
+ gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 1 -maf 0.1' % (flat_files('mapping'),
+ this_dataset.group.name,
+ flat_files('mapping'),
+ this_dataset.group.name)
+ if covariates != "":
+ gemma_command += ' -c %s/%s_covariates.txt -outdir %s -o %s_output' % (flat_files('mapping'),
+ this_dataset.group.name,
+ webqtlConfig.GENERATED_IMAGE_DIR,
+ this_dataset.group.name)
else:
- logger.debug("FLAT FILES:", flat_files('mapping'))
- if use_loco:
- generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json --loco ' + chr_list_string + ' -- -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -gk -debug > /home/zas1024/tmp/gn2/K.json' % (flat_files('genotype/bimbam'),
- this_dataset.group.name,
- flat_files('genotype/bimbam'),
- this_dataset.group.name,
- flat_files('genotype/bimbam'),
- this_dataset.group.name)
- logger.debug("k_command:" + generate_k_command)
- os.system(generate_k_command)
-
- run_loco_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input /home/zas1024/tmp/gn2/K.json -- -g %s/%s_geno.txt -p %s/%s_pheno.txt -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > /home/zas1024/tmp/gn2/GWA.json' % (flat_files('genotype/bimbam'),
- this_dataset.group.name,
- flat_files('genotype/bimbam'),
- this_dataset.group.name,
- flat_files('mapping'),
- this_dataset.group.name,
- flat_files('genotype/bimbam'),
- this_dataset.group.name)
- os.system(run_loco_command)
- else:
- gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 1 -maf 0.1 -c %s/%s_covariates.txt -outdir %s -debug -o %s_output' % (flat_files('genotype/bimbam'),
- this_dataset.group.name,
- flat_files('genotype/bimbam'),
- this_dataset.group.name,
- flat_files('genotype/bimbam'),
- this_dataset.group.name,
- flat_files('genotype/bimbam'),
- this_dataset.group.name,
- flat_files('mapping'),
- this_dataset.group.name,
- webqtlConfig.GENERATED_IMAGE_DIR,
- this_dataset.group.name)
- else:
- if method == "gemma":
#gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -o %s_output' % (flat_files('mapping'),
- gemma_command = GEMMA_COMMAND + ' -bfile %s/%s -k %s/%s.cXX.txt -lmm 1 -maf 0.1 -outdir %s -o %s_output' % (flat_files('mapping'),
+ gemma_command += ' -outdir %s -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
+ this_dataset.group.name)
+ else:
+ if use_loco == "True":
+ k_output_filename = this_dataset.group.name + "_K_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
+ generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json --loco ' + chr_list_string + ' -- -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -gk -debug > /home/zas1024/tmp/gn2/%s.json' % (flat_files('genotype/bimbam'),
this_dataset.group.name,
- flat_files('mapping'),
+ flat_files('genotype/bimbam'),
+ this_dataset.group.name,
+ flat_files('genotype/bimbam'),
this_dataset.group.name,
- webqtlConfig.GENERATED_IMAGE_DIR,
+ k_output_filename)
+ logger.debug("k_command:" + generate_k_command)
+ os.system(generate_k_command)
+
+ gemma_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input /home/zas1024/tmp/gn2/%s.json -- -g %s/%s_geno.txt -p %s/%s_pheno.txt' % (k_output_filename,
+ flat_files('genotype/bimbam'),
+ this_dataset.group.name,
+ flat_files('genotype/bimbam'),
this_dataset.group.name)
- else:
- if use_loco:
- generate_k_command = GEMMA_WRAPPER_COMMAND + ' --json --loco ' + chr_list_string + ' -- -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -gk -debug > /home/zas1024/tmp/gn2/K.json' % (flat_files('genotype/bimbam'),
- this_dataset.group.name,
- flat_files('genotype/bimbam'),
- this_dataset.group.name,
- flat_files('genotype/bimbam'),
- this_dataset.group.name)
- logger.debug("k_command:" + generate_k_command)
- os.system(generate_k_command)
-
- run_loco_command = GEMMA_WRAPPER_COMMAND + ' --json --loco --input /home/zas1024/tmp/gn2/K.json -- -g %s/%s_geno.txt -p %s/%s_pheno.txt -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > /home/zas1024/tmp/gn2/GWA.json' % (flat_files('genotype/bimbam'),
- this_dataset.group.name,
- flat_files('genotype/bimbam'),
- this_dataset.group.name,
- flat_files('mapping'),
- this_dataset.group.name,
- flat_files('genotype/bimbam'),
- this_dataset.group.name)
- os.system(run_loco_command)
+
+ gwa_output_filename = this_dataset.group.name + "_GWA_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
+ if covariates != "":
+ gemma_command += ' -c %s/%s_covariates.txt -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > /home/zas1024/tmp/gn2/%s.json' % (flat_files('mapping'),
+ this_dataset.group.name,
+ flat_files('genotype/bimbam'),
+ this_dataset.group.name,
+ gwa_output_filename)
else:
- #gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.sXX.txt -lmm 1 -maf 0.1 -o %s_output' % (flat_files('genotype/bimbam'),
- gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 1 -maf 0.1 -outdir %s -debug -o %s_output' % (flat_files('genotype/bimbam'),
+ gemma_command += ' -a %s/%s_snps.txt -lmm 1 -maf 0.1 -debug > /home/zas1024/tmp/gn2/GWA.json' % (flat_files('genotype/bimbam'),
+ this_dataset.group.name)
+
+ else:
+ gemma_command = GEMMA_COMMAND + ' -g %s/%s_geno.txt -p %s/%s_pheno.txt -a %s/%s_snps.txt -k %s/%s.cXX.txt -lmm 1 -maf 0.1' % (flat_files('genotype/bimbam'),
this_dataset.group.name,
flat_files('genotype/bimbam'),
this_dataset.group.name,
flat_files('genotype/bimbam'),
this_dataset.group.name,
flat_files('genotype/bimbam'),
- this_dataset.group.name,
- webqtlConfig.GENERATED_IMAGE_DIR,
this_dataset.group.name)
- logger.debug("gemma_command:" + gemma_command)
+ if covariates != "":
+ gemma_command += ' -c %s/%s_covariates.txt -outdir %s -debug -o %s_output' % (flat_files('mapping'),
+ this_dataset.group.name,
+ webqtlConfig.GENERATED_IMAGE_DIR,
+ this_dataset.group.name)
+ else:
+ gemma_command += ' -outdir %s -debug -o %s_output' % (webqtlConfig.GENERATED_IMAGE_DIR,
+ this_dataset.group.name)
+
+ logger.debug("gemma_command:" + gemma_command)
os.system(gemma_command)
- marker_obs = parse_gemma_output(this_dataset)
+ if use_loco == "True":
+ marker_obs = parse_loco_output(this_dataset, gwa_output_filename)
+ else:
+ marker_obs = parse_gemma_output(this_dataset)
return marker_obs
@@ -217,3 +197,46 @@ def parse_gemma_output(this_dataset):
p_values.append(float(line.split("\t")[10]))
return marker_obs
+
+def parse_loco_output(this_dataset, gwa_output_filename):
+
+ output_filelist = []
+ with open("/home/zas1024/tmp/gn2/" + gwa_output_filename + ".json") as data_file:
+ data = json.load(data_file)
+
+ files = data['files']
+ for file in files:
+ output_filelist.append(file[2])
+
+ included_markers = []
+ p_values = []
+ marker_obs = []
+ previous_chr = 0
+
+ for this_file in output_filelist:
+ #with open("/home/zas1024/gene/wqflask/output/{}_output.assoc.txt".format(this_dataset.group.name)) as output_file:
+ with open(this_file) as output_file:
+ for line in output_file:
+ if line.startswith("chr"):
+ continue
+ else:
+ marker = {}
+ marker['name'] = line.split("\t")[1]
+ if line.split("\t")[0] != "X" and line.split("\t")[0] != "X/Y":
+ marker['chr'] = int(line.split("\t")[0])
+ else:
+ marker['chr'] = line.split("\t")[0]
+ marker['Mb'] = float(line.split("\t")[2]) / 1000000
+ marker['p_value'] = float(line.split("\t")[10])
+ if math.isnan(marker['p_value']) or (marker['p_value'] <= 0):
+ marker['lod_score'] = 0
+ #marker['lrs_value'] = 0
+ else:
+ marker['lod_score'] = -math.log10(marker['p_value'])
+ #marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
+ marker_obs.append(marker)
+
+ included_markers.append(line.split("\t")[1])
+ p_values.append(float(line.split("\t")[10]))
+
+ return marker_obs \ No newline at end of file
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 07:46:44 +0000