diff options
Diffstat (limited to 'wqflask/utility')
| -rw-r--r-- | wqflask/utility/Plot.py | 8 | ||||
| -rwxr-xr-x | wqflask/utility/benchmark.py | 8 | ||||
| -rw-r--r-- | wqflask/utility/chunks.py | 10 | ||||
| -rwxr-xr-x | wqflask/utility/corr_result_helpers.py | 18 | ||||
| -rw-r--r-- | wqflask/utility/genofile_parser.py | 4 | ||||
| -rwxr-xr-x | wqflask/utility/temp_data.py | 6 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 4 | ||||
| -rwxr-xr-x | wqflask/utility/webqtlUtil.py | 8 |
8 files changed, 33 insertions, 33 deletions
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py index 444c71c9..063de387 100644 --- a/wqflask/utility/Plot.py +++ b/wqflask/utility/Plot.py @@ -282,11 +282,11 @@ def gpercentile(lst2, np): def find_outliers(vals): """Calculates the upper and lower bounds of a set of sample/case values - - + + >>> find_outliers([3.504, 5.234, 6.123, 7.234, 3.542, 5.341, 7.852, 4.555, 12.537]) (11.252500000000001, 0.5364999999999993) - + >>> >>> find_outliers([9,12,15,17,31,50,7,5,6,8]) (32.0, -8.0) @@ -294,7 +294,7 @@ def find_outliers(vals): which code that calls it will have to deal with. >>> find_outliers([]) (None, None) - + """ print("xerxes vals is:", pf(vals)) diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py index 182187ae..d5b32703 100755 --- a/wqflask/utility/benchmark.py +++ b/wqflask/utility/benchmark.py @@ -7,7 +7,7 @@ import time class Bench(object): entries = collections.OrderedDict() - + def __init__(self, name=None): self.name = name @@ -26,10 +26,10 @@ class Bench(object): time_taken = time.time() - self.start_time print(" %s took: %f seconds" % (name, (time_taken))) - + if self.name: Bench.entries[self.name] = Bench.entries.get(self.name, 0) + time_taken - + @classmethod def report(cls): @@ -39,7 +39,7 @@ class Bench(object): percent = int(round((time_taken/total_time) * 100)) print("[{}%] {}: {}".format(percent, name, time_taken)) print() - + def reset(cls): """Reset the entries""" cls.entries = collections.OrderedDict()
\ No newline at end of file diff --git a/wqflask/utility/chunks.py b/wqflask/utility/chunks.py index 9565fb96..b0e33c08 100644 --- a/wqflask/utility/chunks.py +++ b/wqflask/utility/chunks.py @@ -6,21 +6,21 @@ import time def divide_into_chunks(the_list, number_chunks): """Divides a list into approximately number_chunks smaller lists - + >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3) [[1, 2, 7], [3, 22, 8], [5, 22, 333]] - >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 4) + >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 4) [[1, 2, 7], [3, 22, 8], [5, 22, 333]] - >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 5) + >>> divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 5) [[1, 2], [7, 3], [22, 8], [5, 22], [333]] >>> - + """ length = len(the_list) if length == 0: return [[]] - + if length <= number_chunks: number_chunks = length diff --git a/wqflask/utility/corr_result_helpers.py b/wqflask/utility/corr_result_helpers.py index a253026c..ef644d85 100755 --- a/wqflask/utility/corr_result_helpers.py +++ b/wqflask/utility/corr_result_helpers.py @@ -1,16 +1,16 @@ def normalize_values(a_values, b_values): """ Trim two lists of values to contain only the values they both share - + Given two lists of sample values, trim each list so that it contains only the samples that contain a value in both lists. Also returns the number of such samples. - + >>> normalize_values([2.3, None, None, 3.2, 4.1, 5], [3.4, 7.2, 1.3, None, 6.2, 4.1]) ([2.3, 4.1, 5], [3.4, 6.2, 4.1], 3) - + """ - + min_length = min(len(a_values), len(b_values)) a_new = [] b_new = [] @@ -18,10 +18,10 @@ def normalize_values(a_values, b_values): if a_values[counter] and b_values[counter]: a_new.append(a_values[counter]) b_new.append(b_values[counter]) - + num_overlap = len(a_new) assert num_overlap == len(b_new), "Lengths should be the same" - + return a_new, b_new, num_overlap @@ -37,16 +37,16 @@ def common_keys(a_samples, b_samples): def normalize_values_with_samples(a_samples, b_samples): common_samples = common_keys(a_samples, b_samples) - + a_new = {} b_new = {} for sample in common_samples: a_new[sample] = a_samples[sample] b_new[sample] = b_samples[sample] - + num_overlap = len(a_new) assert num_overlap == len(b_new), "Lengths should be the same" - + return a_new, b_new, num_overlap diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py index 67b84dc9..7149e560 100644 --- a/wqflask/utility/genofile_parser.py +++ b/wqflask/utility/genofile_parser.py @@ -28,10 +28,10 @@ class ConvertGenoFile(object): self.mb_exists = False self.cm_exists = False self.markers = [] - + self.latest_row_pos = None self.latest_col_pos = None - + self.latest_row_value = None self.latest_col_value = None self.input_fh = open(input_file) diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py index 004d45c6..5bf700c9 100755 --- a/wqflask/utility/temp_data.py +++ b/wqflask/utility/temp_data.py @@ -4,16 +4,16 @@ from redis import Redis import simplejson as json class TempData(object): - + def __init__(self, temp_uuid): self.temp_uuid = temp_uuid self.redis = Redis() self.key = "tempdata:{}".format(self.temp_uuid) - + def store(self, field, value): self.redis.hset(self.key, field, value) self.redis.expire(self.key, 60*15) # Expire in 15 minutes - + def get_all(self): return self.redis.hgetall(self.key) diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 955f3bdd..6e9f6d4a 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -35,7 +35,7 @@ def get_setting(command_id,guess=None): return command else: return None - + # ---- Check whether environment exists # sys.stderr.write("Looking for "+command_id+"\n") command = value(os.environ.get(command_id)) @@ -128,7 +128,7 @@ def locate_ignore_error(name, subdir=None): def tempdir(): return valid_path(get_setting("TEMPDIR","/tmp")) - + # Cached values WEBSERVER_MODE = get_setting('WEBSERVER_MODE') LOGGING = get_setting('LOGGING') diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py index 1108614b..4fc978f5 100755 --- a/wqflask/utility/webqtlUtil.py +++ b/wqflask/utility/webqtlUtil.py @@ -129,7 +129,7 @@ def inverseCumul(p): return None if p>0 and p < 1: - e = 0.5 * erfcc(-x/sqrt(2)) - p + e = 0.5 * erfcc(-x/sqrt(2)) - p u = e * sqrt(2*pi) * exp(x*x/2) x = x - u/(1 + x*u/2) return x @@ -318,10 +318,10 @@ def FloatList2String(lst): def ListNotNull(lst): '''Obsolete - Use built in function any (or all or whatever) - - + + Determine if the elements in a list are all null - + ''' for item in lst: if item is not None: |