diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/wqflask/marker_regression/marker_regression.py | 24 |
1 files changed, 13 insertions, 11 deletions
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index abd1ce85..39d7c78a 100644 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -39,6 +39,7 @@ from wqflask.marker_regression import gemma_mapping from utility.tools import locate, locate_ignore_error, PYLMM_COMMAND, GEMMA_COMMAND, PLINK_COMMAND from utility.external import shell +from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR class MarkerRegression(object): @@ -324,7 +325,7 @@ class MarkerRegression(object): self.gen_pheno_txt_file_plink(pheno_filename = output_filename) - rqtl_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (self.dataset.group.name, self.dataset.group.name, webqtlConfig.TMPDIR, plink_output_filename, self.this_trait.name, self.maf, webqtlConfig.TMPDIR, plink_output_filename) + rqtl_command = './plink --noweb --ped %s.ped --no-fid --no-parents --no-sex --no-pheno --map %s.map --pheno %s/%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (self.dataset.group.name, self.dataset.group.name, TMPDIR, plink_output_filename, self.this_trait.name, self.maf, TMPDIR, plink_output_filename) os.system(rqtl_command) @@ -381,10 +382,11 @@ class MarkerRegression(object): calc_genoprob = ro.r["calc.genoprob"] # Map the calc.genoprob function read_cross = ro.r["read.cross"] # Map the read.cross function write_cross = ro.r["write.cross"] # Map the write.cross function - GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the GENOtoCSVR function + GENOtoCSVR = ro.r["GENOtoCSVR"] # Map the local GENOtoCSVR function - genofilelocation = locate(self.dataset.group.name + ".geno", "genotype") - crossfilelocation = locate(self.dataset.group.name + ".cross", "genotype") + crossname = self.dataset.group.name + genofilelocation = locate(crossname + ".geno", "genotype") + crossfilelocation = TMPDIR + crossname + ".cross" #print("Conversion of geno to cross at location:", genofilelocation, " to ", crossfilelocation) @@ -411,7 +413,7 @@ class MarkerRegression(object): #print("Pair scan results:", result_data_frame) self.pair_scan_filename = webqtlUtil.genRandStr("scantwo_") + ".png" - png(file=webqtlConfig.TMPDIR+self.pair_scan_filename) + png(file=TMPDIR+self.pair_scan_filename) plot(result_data_frame) dev_off() @@ -521,8 +523,8 @@ class MarkerRegression(object): self.gen_pheno_txt_file_plink(pheno_filename = plink_output_filename) - plink_command = PLINK_COMMAND + ' --noweb --bed %s/%s.bed --bim %s/%s.bim --fam %s/%s.fam --no-fid --no-parents --no-sex --no-pheno --pheno %s%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (PLINK_PATH, self.dataset.group.name, PLINK_PATH, self.dataset.group.name, PLINK_PATH, self.dataset.group.name, webqtlConfig.TMPDIR, plink_output_filename, self.this_trait.name, self.maf, webqtlConfig.TMPDIR, plink_output_filename) - #print("plink_command:", plink_command) + plink_command = PLINK_COMMAND + ' --noweb --ped %s/%s.ped --no-fid --no-parents --no-sex --no-pheno --map %s/%s.map --pheno %s%s.txt --pheno-name %s --maf %s --missing-phenotype -9999 --out %s%s --assoc ' % (PLINK_PATH, self.dataset.group.name, PLINK_PATH, self.dataset.group.name, TMPDIR, plink_output_filename, self.this_trait.name, self.maf, TMPDIR, plink_output_filename) + print("plink_command:", plink_command) os.system(plink_command) @@ -543,7 +545,7 @@ class MarkerRegression(object): def gen_pheno_txt_file_plink(self, pheno_filename = ''): ped_sample_list = self.get_samples_from_ped_file() - output_file = open("%s%s.txt" % (webqtlConfig.TMPDIR, pheno_filename), "wb") + output_file = open("%s%s.txt" % (TMPDIR, pheno_filename), "wb") header = 'FID\tIID\t%s\n' % self.this_trait.name output_file.write(header) @@ -578,7 +580,7 @@ class MarkerRegression(object): def gen_pheno_txt_file_rqtl(self, pheno_filename = ''): ped_sample_list = self.get_samples_from_ped_file() - output_file = open("%s%s.txt" % (webqtlConfig.TMPDIR, pheno_filename), "wb") + output_file = open("%s%s.txt" % (TMPDIR, pheno_filename), "wb") header = 'FID\tIID\t%s\n' % self.this_trait.name output_file.write(header) @@ -720,7 +722,7 @@ class MarkerRegression(object): threshold_p_value = 0.01 - result_fp = open("%s%s.qassoc"% (webqtlConfig.TMPDIR, output_filename), "rb") + result_fp = open("%s%s.qassoc"% (TMPDIR, output_filename), "rb") header_line = result_fp.readline()# read header line line = result_fp.readline() @@ -1042,7 +1044,7 @@ def create_snp_iterator_file(group): This function is only called by main below """ raise Exception("Paths are undefined here") - plink_file_base = os.path.join(webqtlConfig.TMPDIR, group) + plink_file_base = os.path.join(TMPDIR, group) plink_input = input.plink(plink_file_base, type='b') data = dict(plink_input = list(plink_input), |