diff options
| -rwxr-xr-x | genotype_files/genotypes/HSNIH.geno | 4 | ||||
| -rwxr-xr-x | wqflask/base/data_set.py | 5 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/marker_regression/marker_regression.py | 4 | ||||
| -rwxr-xr-x | wqflask/wqflask/my_pylmm/data/genofile_parser.py | 10 | ||||
| -rwxr-xr-x | wqflask/wqflask/show_trait/show_trait.py | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/chr_lod_chart.js | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/static/new/javascript/panelutil.js | 2 | ||||
| -rwxr-xr-x | wqflask/wqflask/views.py | 8 |
9 files changed, 22 insertions, 17 deletions
diff --git a/genotype_files/genotypes/HSNIH.geno b/genotype_files/genotypes/HSNIH.geno index 525f0183..1817e252 100755 --- a/genotype_files/genotypes/HSNIH.geno +++ b/genotype_files/genotypes/HSNIH.geno @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:550df9276046d5aef116e9ab3dff6a03a137e74ba0c21cc0ae59d1f83e9b9673 -size 22560 +oid sha256:719bbdea26ebc969ce82bb4f668630e179ddb796e9e4095b44a0fa9b7b9da22d +size 23006 diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py index d6a46c2e..5603fe2e 100755 --- a/wqflask/base/data_set.py +++ b/wqflask/base/data_set.py @@ -158,7 +158,10 @@ class Markers(object): """Todo: Build in cacheing so it saves us reading the same file more than once""" def __init__(self, name): json_data_fh = open(os.path.join(webqtlConfig.NEWGENODIR + name + '.json')) - markers = json.load(json_data_fh) + try: + markers = json.load(json_data_fh) + except: + markers = [] for marker in markers: if (marker['chr'] != "X") and (marker['chr'] != "Y"): diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 760ded7c..b8a41f60 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -63,7 +63,7 @@ def plink_command(default=None): else: None - guess = os.environ.get('HOME')+'/plink' + guess = os.environ.get('HOME')+'/plink_gemma' path = get_setting('PLINK_PATH',default,guess,get_valid_path) plink_command = path+'/plink' return path,plink_command diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py index dc7ebfcc..553b4358 100755 --- a/wqflask/wqflask/marker_regression/marker_regression.py +++ b/wqflask/wqflask/marker_regression/marker_regression.py @@ -74,7 +74,7 @@ class MarkerRegression(object): self.significant = "" self.pair_scan = False # Initializing this since it is checked in views to determine which template to use self.score_type = "LRS" #ZS: LRS or LOD - self.mapping_scale = "megabase" + self.mapping_scale = "physic" self.dataset.group.get_markers() if self.mapping_method == "gemma": @@ -87,7 +87,7 @@ class MarkerRegression(object): results = self.run_rqtl_plink() elif self.mapping_method == "rqtl_geno": self.score_type = "LOD" - self.mapping_scale = "centimorgan" + self.mapping_scale = "morgan" if start_vars['num_perm'] == "": self.num_perm = 0 else: diff --git a/wqflask/wqflask/my_pylmm/data/genofile_parser.py b/wqflask/wqflask/my_pylmm/data/genofile_parser.py index 9191f345..61a00136 100755 --- a/wqflask/wqflask/my_pylmm/data/genofile_parser.py +++ b/wqflask/wqflask/my_pylmm/data/genofile_parser.py @@ -65,11 +65,11 @@ class ConvertGenoFile(object): self.configurations = {} #self.skipped_cols = 3 - if self.input_file.endswith(".geno.gz"): - print("self.input_file: ", self.input_file) - self.input_fh = gzip.open(self.input_file) - else: - self.input_fh = open(self.input_file) + #if self.input_file.endswith(".geno.gz"): + # print("self.input_file: ", self.input_file) + # self.input_fh = gzip.open(self.input_file) + #else: + self.input_fh = open(self.input_file) with open(self.output_file, "w") as self.output_fh: #if self.file_type == "geno": diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index 850c99a7..aa6f9562 100755 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -167,7 +167,7 @@ class ShowTrait(object): return False def check_pylmm_rqtl(): - if os.path.isfile(webqtlConfig.GENODIR+self.dataset.group.name+".geno"): + if os.path.isfile(webqtlConfig.GENODIR+self.dataset.group.name+".geno") and (os.path.getsize(webqtlConfig.NEWGENODIR+self.dataset.group.name+".json") > 0): return True else: return False diff --git a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js index 60878978..c6fb52d8 100644 --- a/wqflask/wqflask/static/new/javascript/chr_lod_chart.js +++ b/wqflask/wqflask/static/new/javascript/chr_lod_chart.js @@ -119,7 +119,7 @@ Chr_Lod_Chart = (function() { }; Chr_Lod_Chart.prototype.create_scales = function() { - if (this.mappingScale == "centimorgan") { + if (this.mappingScale == "morgan") { max_pos = 0 for (i = 0, len = this.these_results.length; i < len; i++) { marker = this.these_results[i] diff --git a/wqflask/wqflask/static/new/javascript/panelutil.js b/wqflask/wqflask/static/new/javascript/panelutil.js index 5a931f7d..4c8e77ba 100644 --- a/wqflask/wqflask/static/new/javascript/panelutil.js +++ b/wqflask/wqflask/static/new/javascript/panelutil.js @@ -157,7 +157,7 @@ chrscales = function(data, width, chrGap, leftMargin, pad4heatmap, mappingScale) data.chrEnd.push(cur + w); cur = data.chrEnd[i] + chrGap; - if (mappingScale == "centimorgan") { + if (mappingScale == "morgan") { max_pos = d3.max(data.posByChr[chr[0]]) console.log("max_pos:", max_pos) data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], max_pos]).range([data.chrStart[i], data.chrEnd[i]]); diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index ba96428d..588433f0 100755 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -335,6 +335,8 @@ def marker_regression_page(): 'trait_id', 'dataset', 'method', + 'mapping_scale', + 'score_type', 'suggestive', 'num_perm', 'maf', @@ -352,7 +354,7 @@ def marker_regression_page(): if key in wanted or key.startswith(('value:')): start_vars[key] = value - version = "v4" + version = "v1" key = "marker_regression:{}:".format(version) + json.dumps(start_vars, sort_keys=True) print("key is:", pf(key)) with Bench("Loading cache"): @@ -404,8 +406,8 @@ def marker_regression_page(): result['pair_scan_array'] = bytesarray rendered_template = render_template("pair_scan_results.html", **result) else: - #rendered_template = render_template("marker_regression.html", **result) - rendered_template = render_template("marker_regression_gn1.html", **result) + rendered_template = render_template("marker_regression.html", **result) + #rendered_template = render_template("marker_regression_gn1.html", **result) return rendered_template |