diff options
Diffstat (limited to 'wqflask')
| -rwxr-xr-x | wqflask/base/data_set.py | 17 | ||||
| -rwxr-xr-x | wqflask/base/webqtlConfig.py | 2 | ||||
| -rwxr-xr-x | wqflask/maintenance/get_group_samplelists.py | 18 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 17 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 28 | ||||
| -rwxr-xr-x | wqflask/wqflask/templates/show_trait_mapping_tools.html | 13 |
6 files changed, 82 insertions, 13 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index 36f7d036..414cc71a 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -371,7 +371,7 @@ class DatasetGroup(object): self.parlist = [maternal, paternal] def get_samplelist(self): - key = "samplelist:v4:" + self.name + key = "samplelist:v2:" + self.name print("key is:", key) with Bench("Loading cache"): result = Redis.get(key) @@ -384,9 +384,18 @@ class DatasetGroup(object): print(" self.samplelist: ", self.samplelist) else: print("Cache not hit") - try: - self.samplelist = get_group_samplelists.get_samplelist(self.name + ".geno") - except IOError: + + from utility.tools import plink_command + PLINK_PATH,PLINK_COMMAND = plink_command() + + geno_file_path = webqtlConfig.GENODIR+self.name+".geno" + plink_file_path = PLINK_PATH+"/"+self.name+".fam" + + if os.path.isfile(plink_file_path): + self.samplelist = get_group_samplelists.get_samplelist("plink", plink_file_path) + elif os.path.isfile(geno_file_path): + self.samplelist = get_group_samplelists.get_samplelist("geno", geno_file_path) + else: self.samplelist = None print("after get_samplelist") Redis.set(key, json.dumps(self.samplelist)) diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 48d8cd0a..330fec56 100755 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -53,7 +53,7 @@ GNROOT = "/home/zas1024/gene/" # Will remove this and dependent items later SECUREDIR = GNROOT + 'secure/' COMMON_LIB = GNROOT + 'support/admin' HTMLPATH = GNROOT + 'genotype_files/' -PYLMM_PATH = '/home/zas1024/plink/' +PYLMM_PATH = '/home/zas1024/plink_gemma/' SNP_PATH = '/home/zas1024/snps/' IMGDIR = GNROOT + '/wqflask/wqflask/images/' IMAGESPATH = HTMLPATH + 'images/' diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py index c9ec3872..3b3930ad 100755 --- a/wqflask/maintenance/get_group_samplelists.py +++ b/wqflask/maintenance/get_group_samplelists.py @@ -17,8 +17,13 @@ def process_genofiles(geno_dir=webqtlConfig.GENODIR): sample_list = get_samplelist(geno_file) -def get_samplelist(geno_file): - genofilename = os.path.join(webqtlConfig.GENODIR, geno_file) +def get_samplelist(file_type, geno_file): + if file_type == "geno": + return get_samplelist_from_geno(geno_file) + elif file_type == "plink": + return get_samplelist_from_plink(geno_file) + +def get_samplelist_from_geno(genofilename): if os.path.isfile(genofilename + '.gz'): genofilename += '.gz' genofile = gzip.open(genofilename) @@ -41,3 +46,12 @@ def get_samplelist(geno_file): samplelist = headers[3:] return samplelist +def get_samplelist_from_plink(genofilename): + genofile = open(genofilename) + + samplelist = [] + for line in genofile: + line = line.split("\t") + samplelist.append(line[0]) + + return samplelist \ No newline at end of file diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 6e35f00a..760ded7c 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -66,4 +66,19 @@ def plink_command(default=None): guess = os.environ.get('HOME')+'/plink' path = get_setting('PLINK_PATH',default,guess,get_valid_path) plink_command = path+'/plink' - return path,plink_command \ No newline at end of file + return path,plink_command + +def gemma_command(default=None): + def get_valid_path(path): + """Test for a valid repository""" + if path: + sys.stderr.write("Trying PLINK_PATH in "+path+"\n") + if path and os.path.isfile(path+'/plink'): + return path + else: + None + + guess = os.environ.get('HOME')+'/plink' + path = get_setting('PLINK_PATH',default,guess,get_valid_path) + gemma_command = path+'/gemma' + return path, gemma_command \ No newline at end of file diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 61305e9b..02472267 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -16,6 +16,7 @@ from base import webqtlConfig from base import webqtlCaseData from wqflask.show_trait.SampleList import SampleList from utility import webqtlUtil, Plot, Bunch, helper_functions +from utility.tools import pylmm_command, plink_command from base.trait import GeneralTrait from base import data_set from dbFunction import webqtlDatabaseFunction @@ -23,6 +24,9 @@ from basicStatistics import BasicStatisticsFunctions from pprint import pformat as pf +PYLMM_PATH,PYLMM_COMMAND = pylmm_command() +PLINK_PATH,PLINK_COMMAND = plink_command() + ############################################### # # Todo: Put in security to ensure that user has permission to access confidential data sets @@ -137,12 +141,36 @@ class ShowTrait(object): sample_lists = [group.sample_list for group in self.sample_groups] print("sample_lists is:", pf(sample_lists)) + self.get_mapping_methods() + js_data = dict(sample_group_types = self.sample_group_types, sample_lists = sample_lists, attribute_names = self.sample_groups[0].attributes, temp_uuid = self.temp_uuid) self.js_data = js_data + def get_mapping_methods(self): + '''Only display mapping methods when the dataset group's genotype file exists''' + def check_plink_gemma(): + if (os.path.isfile(PLINK_PATH+"/"+self.dataset.group.name+".bed") and + os.path.isfile(PLINK_PATH+"/"+self.dataset.group.name+".bim") and + os.path.isfile(PLINK_PATH+"/"+self.dataset.group.name+".fam") and + os.path.isfile(PLINK_PATH+"/"+self.dataset.group.name+".map")): + + return True + else: + return False + + def check_pylmm_rqtl(): + if os.path.isfile(webqtlConfig.GENODIR+self.dataset.group.name+".geno"): + return True + else: + return False + + self.use_plink_gemma = check_plink_gemma() + self.use_pylmm_rqtl = check_pylmm_rqtl() + + def read_data(self, include_f1=False): '''read user input data or from trait data and analysis form''' diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html index 1550647a..547da0d0 100755 --- a/wqflask/wqflask/templates/show_trait_mapping_tools.html +++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html @@ -1,20 +1,21 @@ <div> + {% if use_pylmm_rqtl or use_plink_gemma %} <div class="col-xs-6"> <div class="tabbable"> <!-- Only required for left/right tabs --> <ul class="nav nav-pills"> + {% if use_pylmm_rqtl and not use_plink_gemma %} <li class="active"> <a href="#pylmm" data-toggle="tab">pyLMM</a> </li> <li> <a href="#rqtl_geno" data-toggle="tab">rqtl</a> </li> - {% if dataset.group.species != 'human' %} <li> <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a> </li> {% endif %} - {% if dataset.group.species == 'human' %} + {% if use_plink_gemma %} <li> <a href="#plink" data-toggle="tab">PLINK</a> </li> @@ -28,8 +29,8 @@ </ul> <div class="tab-content"> + {% if use_pylmm_rqtl %} <div class="tab-pane active" id="pylmm"> - <div style="padding: 20px" class="form-horizontal"> <div class="mapping_method_fields form-group"> <label for="mapping_permutations" class="col-xs-2 control-label">Permutations</label> @@ -160,7 +161,6 @@ </div> </div> </div> - {% if dataset.group.species != 'human' %} <div class="tab-pane" id="interval_mapping"> <div style="padding: 20px" class="form-horizontal"> <div class="mapping_method_fields form-group"> @@ -214,7 +214,7 @@ </div> </div> {% endif %} - {% if dataset.group.species == 'human' %} + {% if use_plink_gemma %} <div class="tab-pane" id="plink"> <div style="padding: 20px" class="form-horizontal"> <div class="mapping_method_fields form-group"> @@ -272,4 +272,7 @@ <div id="mapping_result_holder_wrapper" style="display:none;"> <div id="mapping_result_holder"></div> </div> + {% else %} + Mapping options are disabled for data not matched with genotypes. + {% endif %} </div> |