SciCodePile/SciCode-Domain-Code

1"keyword","repo_name","file_path","file_extension","file_size","line_count","content","language"
2"Epigenetics","Weikai-47/Pepper_T2T","2. Validation/plot_coverage.depth.py",".py","1742","47","import pandas as pd3import matplotlib.pyplot as plt4plt.rc('font',family='Times New Roman')5import numpy as np6 7data = pd.read_excel('./副本Andean_coverage6.xlsx')8data['ONT_position'] = 09data.columns = ['HiFi_chr','HiFi_start','HiFi_end','HiFi_value','HiFi_position',10                'NGS_chr','NGS_start','NGS_end','NGS_value','NGS_position',11                'ONT_chr','ONT_start','ONT_end','ONT_value','ONT_position']12list_data = list(data.groupby('NGS_chr'))13 14chr_dict = {}15for i in list_data:16    chr_dict[i[0]] = i[1]17 18labels = [0]19count = 020for i in range(1,14):21    for j in ['HiFi_start','NGS_start','ONT_start','HiFi_end','NGS_end','ONT_end']:22        chr_dict['chr{}'.format(i)][j] += count23    count = chr_dict['chr{}'.format(i)].iloc[-1,:]['NGS_end']24    labels.append(count/1000000)25 26data1 = chr_dict['chr1']27for i in range(2,14):28    data1 = pd.concat([data1,chr_dict['chr{}'.format(i)]])29 30for i in ['NGS','ONT','HiFi']:31    data1[i+'_position'] = (data1[i+'_start'].astype('float') + data1[i+'_end'].astype('float'))/2.032 33 34name = ['HiFi','NGS','ONT']35color = ['pink','aqua','lavender']36for i in range(0,3):37    plt.subplot(3, 1, i+1)38    ax = plt.gca()  # gca:get current axis得到当前轴39    # 设置图片的右边框和上边框为不显示40    ax.spines['right'].set_color('none')41    ax.spines['top'].set_color('none')42    print(data1[name[i]+'_value'])43    plt.bar(data1[name[i]+'_position'] / 1000000, data1[name[i]+'_value'], width=1.0, color=color[i])44    plt.scatter(data1[name[i]+'_position'] / 1000000, data1[name[i]+'_value'], color='black', s=0.8, alpha=0.6, marker='s')45    plt.ylabel(name[i]+' Sequence Depth', fontsize=14)46    plt.xticks(labels)47plt.show()48","Python"
49"Epigenetics","Weikai-47/Pepper_T2T","SVM-based classifier/2.FeatureImportances.py",".py","1518","39","import numpy as np50from sklearn.svm import SVC51from sklearn.ensemble import RandomForestClassifier, GradientBoostingClassifier52 53 54def stat_feature_importance(X, Y, model, name_list):55    X = np.array(X)56    Y = np.array(Y)57 58    # 训练模型59    model.fit(X, Y)60 61    # 根据模型类型获取特征重要性62    if hasattr(model, 'coef_'):63        # 对于线性模型64        feature_importance = np.abs(model.coef_)65    elif hasattr(model, 'feature_importances_'):66        # 对于支持feature_importances_属性的模型，如RF和Gradient Boosting67        feature_importance = model.feature_importances_68    else:69        raise ValueError(""Model does not have feature importance attribute"")70 71    # 对于线性模型，feature_importance是一个二维数组，我们需要将其转化为一维72    if len(feature_importance.shape) > 1:73        feature_importance = np.mean(feature_importance, axis=0)74 75    # 创建一个字典来存储特征名称和它们的重要性76    feature_importance_dict = dict(zip(name_list, feature_importance))77    # 按重要性降序排序字典78    sorted_feature_importance = dict(sorted(feature_importance_dict.items(), key=lambda item: item[1], reverse=True))79 80    with open(""../features_importance.csv"", ""w"") as f:81        # 输出排序后的特征重要性82        for feature, importance in sorted_feature_importance.items():83            print(f""{feature}: {importance}"")84            f.write(feature + "","" + str(importance) + '\n')85 86 87","Python"
88"Epigenetics","Weikai-47/Pepper_T2T","SVM-based classifier/1.GridSearch.py",".py","5067","150","import numpy as np89import pandas as pd90from sklearn.model_selection import cross_val_score, GridSearchCV91from sklearn.svm import SVC92from sklearn.ensemble import RandomForestClassifier93from sklearn.neighbors import KNeighborsClassifier94from sklearn.ensemble import GradientBoostingClassifier95import Visualization as vis96from sklearn.model_selection import StratifiedKFold97from sklearn.feature_selection import RFECV98from Feature_Importance import stat_feature_importance99 100# (1) load and transform the data101data = pd.read_excel(""../CBGs_cnv.xlsx"")102data1 = pd.read_excel(""../STab.356_reseq.xlsx"")[[""Sample name"",""Capsaicinoids content (mg/kg DW)""]]103 104index = data.columns105data = pd.DataFrame(np.array(data).T)106data.index = index107data = data.reset_index()108data.columns = data.iloc[1,:]109data = data.iloc[2:,:]110data = data.merge(data1,left_on=""Gene"",right_on=""Sample name"")111 112name_list = []113for i in data.columns:114    if i != ""Sample name"":115        name_list.append(i)116 117data = data[name_list]118list1 = [i for i in data.columns]119list1[0] = 'SampleID'120data.columns = list1121data['Capsaicinoids content (mg/kg DW)'] = data['Capsaicinoids content (mg/kg DW)'].astype('float')122data = data[data[""Capsaicinoids content (mg/kg DW)""] >= 0]123 124# split the labels according to the median, so we can get the balanced dataset125C_level = np.array(data['Capsaicinoids content (mg/kg DW)'].astype(float)).tolist()126C_level.sort(reverse=True)127 128def func2(x):129    if x <= C_level[int(len(C_level)/2)]:130        return 0.0131    else:132        return 1.0133 134data['Capsaicinoids content (mg/kg DW)'] = data['Capsaicinoids content (mg/kg DW)'].apply(func2).astype(int)135 136# (2) Features selection137X = data.drop([""SampleID"", ""Capsaicinoids content (mg/kg DW)""], axis=1)138y = data[""Capsaicinoids content (mg/kg DW)""]139 140# 初始化一个SVM分类器141RF = RandomForestClassifier()142# 使用RFECV进行特征选择，以找到最佳特征数量143# StratifiedKFold用于确保每个类的样本比例保持一致144# step表示每次迭代要移除的特征数145# cv代表交叉验证的策略，这里使用5折交叉验证146rfecv = RFECV(estimator=RF, step=1, cv=StratifiedKFold(5), scoring='accuracy')147rfecv.fit(X, y)148 149# 打印出最佳特征数量150print(""Optimal number of features : %d"" % rfecv.n_features_)151 152# 选择特征153X_new = rfecv.transform(X)154 155# 获取被选中的特征的布尔掩码156selected_features_mask = rfecv.support_157 158# 使用布尔掩码来获取被选中的特征名称159selected_features_names = X.columns[selected_features_mask]160 161print(""Selected features names:"")162print(selected_features_names)163 164# (3) Set the parameters for models165models = [166    (""Support Vector Machine (Kernal: linear)"", SVC(), {""C"": [0.0001, 0.001, 0.01, 0.1, 1, 10], ""kernel"": [ ""linear"" ]}),167    (""Random Forest"", RandomForestClassifier(), {""n_estimators"": [10, 50, 100, 150], ""max_depth"": [1, 10, 20, 30], 'max_features':[None, 'sqrt', 'log2']}),168    (""K Nearest Neighbors"", KNeighborsClassifier(), {""n_neighbors"": [3, 5, 7, 10], ""weights"": [""uniform"", ""distance""]}),169    (""Gradient Boosting"", GradientBoostingClassifier(),170     {171         'n_estimators': [10, 50, 100, 150],172         'learning_rate': [0.01, 0.1, 0.2],173         'max_depth': [1, 10, 20, 30],174         'max_features': [None, 'sqrt', 'log2'],175         'subsample': [0.8, 0.9, 1.0]176     }177    )178]179 180acc_scores = {}181precision_scores = {}182recall_scores = {}183 184model_list = []185best_acc = 0186best_model = None187 188# (4) train and evaluate the models189for name, model, params in models:190    # Grid Search the hyperparameters191    grid_search = GridSearchCV(model, params, cv=10, scoring=""accuracy"")192    grid_search.fit(X_new, y)193 194    # print the best hyperparameters195    print(f""{name}:"")196    print(""Best Parameters:"", grid_search.best_params_)197    print(""Best Score:"", grid_search.best_score_)198 199    # use the best hyperparameters to test200    model = grid_search.best_estimator_201    model_list.append(model)202    scores1 = cross_val_score(model, X_new, y, cv=10, scoring=""accuracy"")203    acc_scores[name] = scores1204 205    # output the outcome206    print(""Cross-Validation Scores:"")207    print(""Accuracy:"", scores1.mean())208 209    if scores1.mean() > best_acc:210        best_acc = scores1.mean()211        best_model = model212 213    # Calculate precision and recall214    scores2 = cross_val_score(model, X_new, y, cv=10, scoring=""precision"")215    precision_scores[name] = scores2216 217    # output the outcome218    print(""Cross-Validation Scores:"")219    print(""Precision:"", scores2.mean())220 221    scores3 = cross_val_score(model, X_new, y, cv=10, scoring=""recall"")222    recall_scores[name] = scores3223 224    # output the outcome225    print(""Cross-Validation Scores:"")226    print(""Recall:"", scores3.mean())227 228    print(""-------------------------------"")229 230# (5) Viualization231vis.Visualize_Performance(acc_scores)232 233vis.Draw_ROC_curve(X_new,y,model_list,89)234 235# (6) Statistic Feature importance236stat_feature_importance(X_new,y,best_model,selected_features_names)237","Python"
238"Epigenetics","Weikai-47/Pepper_T2T","SVM-based classifier/0.Count_CNVs.sh",".sh","976","49","fr = open(""/data/pepper/CaT2T.CBGs.bed"",'r')239 240REGIONS = []241 242for line in fr:243    chr = line.strip().split()[0]244    start = line.strip().split()[1]245    end = line.strip().split()[2]246 247    region = chr + "":"" + start + ""-"" + end248 249    REGIONS.append(region)250 251print(REGIONS)252 253 254import glob255 256SAMPLES = [i.split(""/"")[-2] for i in glob.glob(""/data/pepper/*/CRR*_CaT2T.bam"")]257 258print(SAMPLES)259print(""Total sample size: "",len(SAMPLES))260 261 262rule all:263    input:264        expand(""{sample}/{sample}_{region}.CN"",sample=SAMPLES,region=REGIONS)265 266 267rule amycne:268    input:269        gc = ""/data/pepper/gc_content.tab"",270        cov = ""{sample}/{sample}.regions.bed""271    output:272        ""{sample}/{sample}_{region}.CN""273    threads:274        4275    resources:276        mem_mb = 8000277    params:278        ""{region}""279    shell:280        """"""281        python /home/biotools/AMYCNE-master/AMYCNE.py \282        --genotype --gc {input.gc} \283        --coverage  {input.cov} \284        --R {params} > {output}285        """"""286","Shell"
287"Epigenetics","Weikai-47/Pepper_T2T","SVM-based classifier/3.Visualization.py",".py","3172","85","import numpy as np288import pandas as pd289from sklearn.model_selection import cross_val_score, GridSearchCV, cross_val_predict290from sklearn.svm import SVC291from sklearn.ensemble import RandomForestClassifier292from sklearn.metrics import accuracy_score, precision_score, recall_score, f1_score293from sklearn.neighbors import KNeighborsClassifier294from sklearn.ensemble import GradientBoostingClassifier295import matplotlib.pyplot as plt296import seaborn as sns297from sklearn.metrics import precision_score, recall_score298from sklearn.metrics import roc_curve, auc299from sklearn.model_selection import train_test_split300 301def Visualize_Performance(acc_scores):302    # Generate some random data to represent in the boxplot303    np.random.seed(10)304    data = pd.DataFrame(acc_scores)305 306    # Set the style of the seaborn library307    sns.set_style(""whitegrid"")308 309    # Create a figure and a set of subplots310    plt.figure(figsize=(10, 6))311 312    # Create the boxplot with additional parameters for better aesthetics313    sns.boxplot(data=data,314                showmeans=True,315                meanprops={""marker"": ""o"",316                           ""markerfacecolor"": ""white"",317                           ""markeredgecolor"": ""black"",318                           ""markersize"": ""10""})319 320    # Set the labels and title321    plt.xlabel('Prediction Algorithms', fontsize=14)322    plt.ylabel('Accuracy', fontsize=14)323 324    # Improve the aesthetics of the plot axes325    plt.tick_params(axis='both', which='major', labelsize=12)326 327    # Show the plot328    plt.show()329 330def Draw_ROC_curve(X,Y,model_list,random_state):331    # (1) split the train dataset and test dataset332    X_train, X_test, y_train, y_test = train_test_split(X, Y, test_size=0.2, random_state=random_state)333 334    # (2) 建立model，绘制ROC曲线335    SVM_model = model_list[0]336    RF_model = model_list[1]337    KNN_model = model_list[2]338    GBoost_model = model_list[3]339 340    # 训练模型341    SVM_model.fit(X_train, y_train)342    RF_model.fit(X_train, y_train)343    KNN_model.fit(X_train, y_train)344    GBoost_model.fit(X_train, y_train)345 346    # 计算各个模型的概率预测值并绘制ROC曲线347    models = [SVM_model, RF_model, KNN_model, GBoost_model]348    model_names = ['SVM', 'Random Forest', 'K-Nearest Neighbors', 'Gradient Boosting']349 350    plt.figure()351    for model, model_name in zip(models, model_names):352        if isinstance(model, RandomForestClassifier) or isinstance(model, KNeighborsClassifier):353            y_pred_proba = model.predict_proba(X_test)[:, 1]  # 使用predict_proba获取概率值354        else:355            y_pred_proba = model.decision_function(X_test)356 357        fpr, tpr, thresholds = roc_curve(y_test, y_pred_proba)358        roc_auc = auc(fpr, tpr)359 360        plt.plot(fpr, tpr, lw=2, label=f'{model_name} (AUC = {roc_auc:.2f})')361 362    plt.plot([0, 1], [0, 1], color='navy', lw=2, linestyle='--')363    plt.xlim([0.0, 1.0])364    plt.ylim([0.0, 1.05])365    plt.xlabel('False Positive Rate')366    plt.ylabel('True Positive Rate')367    plt.title('Receiver Operating Characteristic (ROC) Curves')368    plt.legend(loc='lower right')369    plt.show()370    371","Python"
372"Epigenetics","epiviz/epiviz","closure-library/closure/bin/scopify.py",".py","6785","222","#!/usr/bin/python373#374# Copyright 2010 The Closure Library Authors. All Rights Reserved.375#376# Licensed under the Apache License, Version 2.0 (the ""License"");377# you may not use this file except in compliance with the License.378# You may obtain a copy of the License at379#380#      http://www.apache.org/licenses/LICENSE-2.0381#382# Unless required by applicable law or agreed to in writing, software383# distributed under the License is distributed on an ""AS-IS"" BASIS,384# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.385# See the License for the specific language governing permissions and386# limitations under the License.387 388 389""""""Automatically converts codebases over to goog.scope.390 391Usage:392cd path/to/my/dir;393../../../../javascript/closure/bin/scopify.py394 395Scans every file in this directory, recursively. Looks for existing396goog.scope calls, and goog.require'd symbols. If it makes sense to397generate a goog.scope call for the file, then we will do so, and398try to auto-generate some aliases based on the goog.require'd symbols.399 400Known Issues:401 402  When a file is goog.scope'd, the file contents will be indented +2.403  This may put some lines over 80 chars. These will need to be fixed manually.404 405  We will only try to create aliases for capitalized names. We do not check406  to see if those names will conflict with any existing locals.407 408  This creates merge conflicts for every line of every outstanding change.409  If you intend to run this on your codebase, make sure your team members410  know. Better yet, send them this script so that they can scopify their411  outstanding changes and ""accept theirs"".412 413  When an alias is ""captured"", it can no longer be stubbed out for testing.414  Run your tests.415 416""""""417 418__author__ = 'nicksantos@google.com (Nick Santos)'419 420import os.path421import re422import sys423 424REQUIRES_RE = re.compile(r""goog.require\('([^']*)'\)"")425 426# Edit this manually if you want something to ""always"" be aliased.427# TODO(nicksantos): Add a flag for this.428DEFAULT_ALIASES = {}429 430def Transform(lines):431  """"""Converts the contents of a file into javascript that uses goog.scope.432 433  Arguments:434    lines: A list of strings, corresponding to each line of the file.435  Returns:436    A new list of strings, or None if the file was not modified.437  """"""438  requires = []439 440  # Do an initial scan to be sure that this file can be processed.441  for line in lines:442    # Skip this file if it has already been scopified.443    if line.find('goog.scope') != -1:444      return None445 446    # If there are any global vars or functions, then we also have447    # to skip the whole file. We might be able to deal with this448    # more elegantly.449    if line.find('var ') == 0 or line.find('function ') == 0:450      return None451 452    for match in REQUIRES_RE.finditer(line):453      requires.append(match.group(1))454 455  if len(requires) == 0:456    return None457 458  # Backwards-sort the requires, so that when one is a substring of another,459  # we match the longer one first.460  for val in DEFAULT_ALIASES.values():461    if requires.count(val) == 0:462      requires.append(val)463 464  requires.sort()465  requires.reverse()466 467  # Generate a map of requires to their aliases468  aliases_to_globals = DEFAULT_ALIASES.copy()469  for req in requires:470    index = req.rfind('.')471    if index == -1:472      alias = req473    else:474      alias = req[(index + 1):]475 476    # Don't scopify lowercase namespaces, because they may conflict with477    # local variables.478    if alias[0].isupper():479      aliases_to_globals[alias] = req480 481  aliases_to_matchers = {}482  globals_to_aliases = {}483  for alias, symbol in aliases_to_globals.items():484    globals_to_aliases[symbol] = alias485    aliases_to_matchers[alias] = re.compile('\\b%s\\b' % symbol)486 487  # Insert a goog.scope that aliases all required symbols.488  result = []489 490  START = 0491  SEEN_REQUIRES = 1492  IN_SCOPE = 2493 494  mode = START495  aliases_used = set()496  insertion_index = None497  num_blank_lines = 0498  for line in lines:499    if mode == START:500      result.append(line)501 502      if re.search(REQUIRES_RE, line):503        mode = SEEN_REQUIRES504 505    elif mode == SEEN_REQUIRES:506      if (line and507          not re.search(REQUIRES_RE, line) and508          not line.isspace()):509        # There should be two blank lines before goog.scope510        result += ['\n'] * 2511        result.append('goog.scope(function() {\n')512        insertion_index = len(result)513        result += ['\n'] * num_blank_lines514        mode = IN_SCOPE515      elif line.isspace():516        # Keep track of the number of blank lines before each block of code so517        # that we can move them after the goog.scope line if necessary.518        num_blank_lines += 1519      else:520        # Print the blank lines we saw before this code block521        result += ['\n'] * num_blank_lines522        num_blank_lines = 0523        result.append(line)524 525    if mode == IN_SCOPE:526      for symbol in requires:527        if not symbol in globals_to_aliases:528          continue529 530        alias = globals_to_aliases[symbol]531        matcher = aliases_to_matchers[alias]532        for match in matcher.finditer(line):533          # Check to make sure we're not in a string.534          # We do this by being as conservative as possible:535          # if there are any quote or double quote characters536          # before the symbol on this line, then bail out.537          before_symbol = line[:match.start(0)]538          if before_symbol.count('""') > 0 or before_symbol.count(""'"") > 0:539            continue540 541          line = line.replace(match.group(0), alias)542          aliases_used.add(alias)543 544      if line.isspace():545        # Truncate all-whitespace lines546        result.append('\n')547      else:548        result.append(line)549 550  if len(aliases_used):551    aliases_used = [alias for alias in aliases_used]552    aliases_used.sort()553    aliases_used.reverse()554    for alias in aliases_used:555      symbol = aliases_to_globals[alias]556      result.insert(insertion_index,557                    'var %s = %s;\n' % (alias, symbol))558    result.append('});  // goog.scope\n')559    return result560  else:561    return None562 563def TransformFileAt(path):564  """"""Converts a file into javascript that uses goog.scope.565 566  Arguments:567    path: A path to a file.568  """"""569  f = open(path)570  lines = Transform(f.readlines())571  if lines:572    f = open(path, 'w')573    for l in lines:574      f.write(l)575    f.close()576 577if __name__ == '__main__':578  args = sys.argv[1:]579  if not len(args):580    args = '.'581 582  for file_name in args:583    if os.path.isdir(file_name):584      for root, dirs, files in os.walk(file_name):585        for name in files:586          if name.endswith('.js') and \587              not os.path.islink(os.path.join(root, name)):588            TransformFileAt(os.path.join(root, name))589    else:590      if file_name.endswith('.js') and \591          not os.path.islink(file_name):592        TransformFileAt(file_name)593","Python"
594"Epigenetics","epiviz/epiviz","closure-library/closure/bin/calcdeps.py",".py","18576","591","#!/usr/bin/env python595#596# Copyright 2006 The Closure Library Authors. All Rights Reserved.597#598# Licensed under the Apache License, Version 2.0 (the ""License"");599# you may not use this file except in compliance with the License.600# You may obtain a copy of the License at601#602#      http://www.apache.org/licenses/LICENSE-2.0603#604# Unless required by applicable law or agreed to in writing, software605# distributed under the License is distributed on an ""AS-IS"" BASIS,606# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.607# See the License for the specific language governing permissions and608# limitations under the License.609 610 611""""""Calculates JavaScript dependencies without requiring Google's build system.612 613This tool is deprecated and is provided for legacy users.614See build/closurebuilder.py and build/depswriter.py for the current tools.615 616It iterates over a number of search paths and builds a dependency tree.  With617the inputs provided, it walks the dependency tree and outputs all the files618required for compilation.619""""""620 621 622 623 624 625try:626  import distutils.version627except ImportError:628  # distutils is not available in all environments629  distutils = None630 631import logging632import optparse633import os634import re635import subprocess636import sys637 638 639_BASE_REGEX_STRING = '^\s*goog\.%s\(\s*[\'""](.+)[\'""]\s*\)'640req_regex = re.compile(_BASE_REGEX_STRING % 'require')641prov_regex = re.compile(_BASE_REGEX_STRING % 'provide')642ns_regex = re.compile('^ns:((\w+\.)*(\w+))$')643version_regex = re.compile('[\.0-9]+')644 645 646def IsValidFile(ref):647  """"""Returns true if the provided reference is a file and exists.""""""648  return os.path.isfile(ref)649 650 651def IsJsFile(ref):652  """"""Returns true if the provided reference is a Javascript file.""""""653  return ref.endswith('.js')654 655 656def IsNamespace(ref):657  """"""Returns true if the provided reference is a namespace.""""""658  return re.match(ns_regex, ref) is not None659 660 661def IsDirectory(ref):662  """"""Returns true if the provided reference is a directory.""""""663  return os.path.isdir(ref)664 665 666def ExpandDirectories(refs):667  """"""Expands any directory references into inputs.668 669  Description:670    Looks for any directories in the provided references.  Found directories671    are recursively searched for .js files, which are then added to the result672    list.673 674  Args:675    refs: a list of references such as files, directories, and namespaces676 677  Returns:678    A list of references with directories removed and replaced by any679    .js files that are found in them. Also, the paths will be normalized.680  """"""681  result = []682  for ref in refs:683    if IsDirectory(ref):684      # Disable 'Unused variable' for subdirs685      # pylint: disable=unused-variable686      for (directory, subdirs, filenames) in os.walk(ref):687        for filename in filenames:688          if IsJsFile(filename):689            result.append(os.path.join(directory, filename))690    else:691      result.append(ref)692  return map(os.path.normpath, result)693 694 695class DependencyInfo(object):696  """"""Represents a dependency that is used to build and walk a tree.""""""697 698  def __init__(self, filename):699    self.filename = filename700    self.provides = []701    self.requires = []702 703  def __str__(self):704    return '%s Provides: %s Requires: %s' % (self.filename,705                                             repr(self.provides),706                                             repr(self.requires))707 708 709def BuildDependenciesFromFiles(files):710  """"""Build a list of dependencies from a list of files.711 712  Description:713    Takes a list of files, extracts their provides and requires, and builds714    out a list of dependency objects.715 716  Args:717    files: a list of files to be parsed for goog.provides and goog.requires.718 719  Returns:720    A list of dependency objects, one for each file in the files argument.721  """"""722  result = []723  filenames = set()724  for filename in files:725    if filename in filenames:726      continue727 728    # Python 3 requires the file encoding to be specified729    if (sys.version_info[0] < 3):730      file_handle = open(filename, 'r')731    else:732      file_handle = open(filename, 'r', encoding='utf8')733 734    try:735      dep = CreateDependencyInfo(filename, file_handle)736      result.append(dep)737    finally:738      file_handle.close()739 740    filenames.add(filename)741 742  return result743 744 745def CreateDependencyInfo(filename, source):746  """"""Create dependency info.747 748  Args:749    filename: Filename for source.750    source: File-like object containing source.751 752  Returns:753    A DependencyInfo object with provides and requires filled.754  """"""755  dep = DependencyInfo(filename)756  for line in source:757    if re.match(req_regex, line):758      dep.requires.append(re.search(req_regex, line).group(1))759    if re.match(prov_regex, line):760      dep.provides.append(re.search(prov_regex, line).group(1))761  return dep762 763 764def BuildDependencyHashFromDependencies(deps):765  """"""Builds a hash for searching dependencies by the namespaces they provide.766 767  Description:768    Dependency objects can provide multiple namespaces.  This method enumerates769    the provides of each dependency and adds them to a hash that can be used770    to easily resolve a given dependency by a namespace it provides.771 772  Args:773    deps: a list of dependency objects used to build the hash.774 775  Raises:776    Exception: If a multiple files try to provide the same namepace.777 778  Returns:779    A hash table { namespace: dependency } that can be used to resolve a780    dependency by a namespace it provides.781  """"""782  dep_hash = {}783  for dep in deps:784    for provide in dep.provides:785      if provide in dep_hash:786        raise Exception('Duplicate provide (%s) in (%s, %s)' % (787            provide,788            dep_hash[provide].filename,789            dep.filename))790      dep_hash[provide] = dep791  return dep_hash792 793 794def CalculateDependencies(paths, inputs):795  """"""Calculates the dependencies for given inputs.796 797  Description:798    This method takes a list of paths (files, directories) and builds a799    searchable data structure based on the namespaces that each .js file800    provides.  It then parses through each input, resolving dependencies801    against this data structure.  The final output is a list of files,802    including the inputs, that represent all of the code that is needed to803    compile the given inputs.804 805  Args:806    paths: the references (files, directories) that are used to build the807      dependency hash.808    inputs: the inputs (files, directories, namespaces) that have dependencies809      that need to be calculated.810 811  Raises:812    Exception: if a provided input is invalid.813 814  Returns:815    A list of all files, including inputs, that are needed to compile the given816    inputs.817  """"""818  deps = BuildDependenciesFromFiles(paths + inputs)819  search_hash = BuildDependencyHashFromDependencies(deps)820  result_list = []821  seen_list = []822  for input_file in inputs:823    if IsNamespace(input_file):824      namespace = re.search(ns_regex, input_file).group(1)825      if namespace not in search_hash:826        raise Exception('Invalid namespace (%s)' % namespace)827      input_file = search_hash[namespace].filename828    if not IsValidFile(input_file) or not IsJsFile(input_file):829      raise Exception('Invalid file (%s)' % input_file)830    seen_list.append(input_file)831    file_handle = open(input_file, 'r')832    try:833      for line in file_handle:834        if re.match(req_regex, line):835          require = re.search(req_regex, line).group(1)836          ResolveDependencies(require, search_hash, result_list, seen_list)837    finally:838      file_handle.close()839    result_list.append(input_file)840 841  # All files depend on base.js, so put it first.842  base_js_path = FindClosureBasePath(paths)843  if base_js_path:844    result_list.insert(0, base_js_path)845  else:846    logging.warning('Closure Library base.js not found.')847 848  return result_list849 850 851def FindClosureBasePath(paths):852  """"""Given a list of file paths, return Closure base.js path, if any.853 854  Args:855    paths: A list of paths.856 857  Returns:858    The path to Closure's base.js file including filename, if found.859  """"""860 861  for path in paths:862    pathname, filename = os.path.split(path)863 864    if filename == 'base.js':865      f = open(path)866 867      is_base = False868 869      # Sanity check that this is the Closure base file.  Check that this870      # is where goog is defined.  This is determined by the @provideGoog871      # flag.872      for line in f:873        if '@provideGoog' in line:874          is_base = True875          break876 877      f.close()878 879      if is_base:880        return path881 882def ResolveDependencies(require, search_hash, result_list, seen_list):883  """"""Takes a given requirement and resolves all of the dependencies for it.884 885  Description:886    A given requirement may require other dependencies.  This method887    recursively resolves all dependencies for the given requirement.888 889  Raises:890    Exception: when require does not exist in the search_hash.891 892  Args:893    require: the namespace to resolve dependencies for.894    search_hash: the data structure used for resolving dependencies.895    result_list: a list of filenames that have been calculated as dependencies.896      This variable is the output for this function.897    seen_list: a list of filenames that have been 'seen'.  This is required898      for the dependency->dependent ordering.899  """"""900  if require not in search_hash:901    raise Exception('Missing provider for (%s)' % require)902 903  dep = search_hash[require]904  if not dep.filename in seen_list:905    seen_list.append(dep.filename)906    for sub_require in dep.requires:907      ResolveDependencies(sub_require, search_hash, result_list, seen_list)908    result_list.append(dep.filename)909 910 911def GetDepsLine(dep, base_path):912  """"""Returns a JS string for a dependency statement in the deps.js file.913 914  Args:915    dep: The dependency that we're printing.916    base_path: The path to Closure's base.js including filename.917  """"""918  return 'goog.addDependency(""%s"", %s, %s);' % (919      GetRelpath(dep.filename, base_path), dep.provides, dep.requires)920 921 922def GetRelpath(path, start):923  """"""Return a relative path to |path| from |start|.""""""924  # NOTE: Python 2.6 provides os.path.relpath, which has almost the same925  # functionality as this function. Since we want to support 2.4, we have926  # to implement it manually. :(927  path_list = os.path.abspath(os.path.normpath(path)).split(os.sep)928  start_list = os.path.abspath(929      os.path.normpath(os.path.dirname(start))).split(os.sep)930 931  common_prefix_count = 0932  for i in range(0, min(len(path_list), len(start_list))):933    if path_list[i] != start_list[i]:934      break935    common_prefix_count += 1936 937  # Always use forward slashes, because this will get expanded to a url,938  # not a file path.939  return '/'.join(['..'] * (len(start_list) - common_prefix_count) +940                  path_list[common_prefix_count:])941 942 943def PrintLine(msg, out):944  out.write(msg)945  out.write('\n')946 947 948def PrintDeps(source_paths, deps, out):949  """"""Print out a deps.js file from a list of source paths.950 951  Args:952    source_paths: Paths that we should generate dependency info for.953    deps: Paths that provide dependency info. Their dependency info should954        not appear in the deps file.955    out: The output file.956 957  Returns:958    True on success, false if it was unable to find the base path959    to generate deps relative to.960  """"""961  base_path = FindClosureBasePath(source_paths + deps)962  if not base_path:963    return False964 965  PrintLine('// This file was autogenerated by calcdeps.py', out)966  excludesSet = set(deps)967 968  for dep in BuildDependenciesFromFiles(source_paths + deps):969    if not dep.filename in excludesSet:970      PrintLine(GetDepsLine(dep, base_path), out)971 972  return True973 974 975def PrintScript(source_paths, out):976  for index, dep in enumerate(source_paths):977    PrintLine('// Input %d' % index, out)978    f = open(dep, 'r')979    PrintLine(f.read(), out)980    f.close()981 982 983def GetJavaVersion():984  """"""Returns the string for the current version of Java installed.""""""985  proc = subprocess.Popen(['java', '-version'], stderr=subprocess.PIPE)986  proc.wait()987  version_line = proc.stderr.read().splitlines()[0]988  return version_regex.search(version_line.decode('utf-8')).group()989 990 991def FilterByExcludes(options, files):992  """"""Filters the given files by the exlusions specified at the command line.993 994  Args:995    options: The flags to calcdeps.996    files: The files to filter.997  Returns:998    A list of files.999  """"""1000  excludes = []1001  if options.excludes:1002    excludes = ExpandDirectories(options.excludes)1003 1004  excludesSet = set(excludes)1005  return [i for i in files if not i in excludesSet]1006 1007 1008def GetPathsFromOptions(options):1009  """"""Generates the path files from flag options.1010 1011  Args:1012    options: The flags to calcdeps.1013  Returns:1014    A list of files in the specified paths. (strings).1015  """"""1016 1017  search_paths = options.paths1018  if not search_paths:1019    search_paths = ['.']  # Add default folder if no path is specified.1020 1021  search_paths = ExpandDirectories(search_paths)1022  return FilterByExcludes(options, search_paths)1023 1024 1025def GetInputsFromOptions(options):1026  """"""Generates the inputs from flag options.1027 1028  Args:1029    options: The flags to calcdeps.1030  Returns:1031    A list of inputs (strings).1032  """"""1033  inputs = options.inputs1034  if not inputs:  # Parse stdin1035    logging.info('No inputs specified. Reading from stdin...')1036    inputs = filter(None, [line.strip('\n') for line in sys.stdin.readlines()])1037 1038  logging.info('Scanning files...')1039  inputs = ExpandDirectories(inputs)1040 1041  return FilterByExcludes(options, inputs)1042 1043 1044def Compile(compiler_jar_path, source_paths, out, flags=None):1045  """"""Prepares command-line call to Closure compiler.1046 1047  Args:1048    compiler_jar_path: Path to the Closure compiler .jar file.1049    source_paths: Source paths to build, in order.1050    flags: A list of additional flags to pass on to Closure compiler.1051  """"""1052  args = ['java', '-jar', compiler_jar_path]1053  for path in source_paths:1054    args += ['--js', path]1055 1056  if flags:1057    args += flags1058 1059  logging.info('Compiling with the following command: %s', ' '.join(args))1060  proc = subprocess.Popen(args, stdout=subprocess.PIPE)1061  (stdoutdata, stderrdata) = proc.communicate()1062  if proc.returncode != 0:1063    logging.error('JavaScript compilation failed.')1064    sys.exit(1)1065  else:1066    out.write(stdoutdata.decode('utf-8'))1067 1068 1069def main():1070  """"""The entrypoint for this script.""""""1071 1072  logging.basicConfig(format='calcdeps.py: %(message)s', level=logging.INFO)1073 1074  usage = 'usage: %prog [options] arg'1075  parser = optparse.OptionParser(usage)1076  parser.add_option('-i',1077                    '--input',1078                    dest='inputs',1079                    action='append',1080                    help='The inputs to calculate dependencies for. Valid '1081                    'values can be files, directories, or namespaces '1082                    '(ns:goog.net.XhrIo).  Only relevant to ""list"" and '1083                    '""script"" output.')1084  parser.add_option('-p',1085                    '--path',1086                    dest='paths',1087                    action='append',1088                    help='The paths that should be traversed to build the '1089                    'dependencies.')1090  parser.add_option('-d',1091                    '--dep',1092                    dest='deps',1093                    action='append',1094                    help='Directories or files that should be traversed to '1095                    'find required dependencies for the deps file. '1096                    'Does not generate dependency information for names '1097                    'provided by these files. Only useful in ""deps"" mode.')1098  parser.add_option('-e',1099                    '--exclude',1100                    dest='excludes',1101                    action='append',1102                    help='Files or directories to exclude from the --path '1103                    'and --input flags')1104  parser.add_option('-o',1105                    '--output_mode',1106                    dest='output_mode',1107                    action='store',1108                    default='list',1109                    help='The type of output to generate from this script. '1110                    'Options are ""list"" for a list of filenames, ""script"" '1111                    'for a single script containing the contents of all the '1112                    'file, ""deps"" to generate a deps.js file for all '1113                    'paths, or ""compiled"" to produce compiled output with '1114                    'the Closure compiler.')1115  parser.add_option('-c',1116                    '--compiler_jar',1117                    dest='compiler_jar',1118                    action='store',1119                    help='The location of the Closure compiler .jar file.')1120  parser.add_option('-f',1121                    '--compiler_flag',1122                    '--compiler_flags', # for backwards compatibility1123                    dest='compiler_flags',1124                    action='append',1125                    help='Additional flag to pass to the Closure compiler. '1126                    'May be specified multiple times to pass multiple flags.')1127  parser.add_option('--output_file',1128                    dest='output_file',1129                    action='store',1130                    help=('If specified, write output to this path instead of '1131                          'writing to standard output.'))1132 1133  (options, args) = parser.parse_args()1134 1135  search_paths = GetPathsFromOptions(options)1136 1137  if options.output_file:1138    out = open(options.output_file, 'w')1139  else:1140    out = sys.stdout1141 1142  if options.output_mode == 'deps':1143    result = PrintDeps(search_paths, ExpandDirectories(options.deps or []), out)1144    if not result:1145      logging.error('Could not find Closure Library in the specified paths')1146      sys.exit(1)1147 1148    return1149 1150  inputs = GetInputsFromOptions(options)1151 1152  logging.info('Finding Closure dependencies...')1153  deps = CalculateDependencies(search_paths, inputs)1154  output_mode = options.output_mode1155 1156  if output_mode == 'script':1157    PrintScript(deps, out)1158  elif output_mode == 'list':1159    # Just print out a dep per line1160    for dep in deps:1161      PrintLine(dep, out)1162  elif output_mode == 'compiled':1163    # Make sure a .jar is specified.1164    if not options.compiler_jar:1165      logging.error('--compiler_jar flag must be specified if --output is '1166                    '""compiled""')1167      sys.exit(1)1168 1169    # User friendly version check.1170    if distutils and not (distutils.version.LooseVersion(GetJavaVersion()) >1171        distutils.version.LooseVersion('1.6')):1172      logging.error('Closure Compiler requires Java 1.6 or higher.')1173      logging.error('Please visit http://www.java.com/getjava')1174      sys.exit(1)1175 1176    Compile(options.compiler_jar, deps, out, options.compiler_flags)1177 1178  else:1179    logging.error('Invalid value for --output flag.')1180    sys.exit(1)1181 1182if __name__ == '__main__':1183  main()1184","Python"
1185"Epigenetics","epiviz/epiviz","closure-library/closure/bin/labs/code/generate_jsdoc_test.py",".py","3494","168","#!/usr/bin/env python1186#1187# Copyright 2013 The Closure Library Authors. All Rights Reserved.1188#1189# Licensed under the Apache License, Version 2.0 (the ""License"");1190# you may not use this file except in compliance with the License.1191# You may obtain a copy of the License at1192#1193#      http://www.apache.org/licenses/LICENSE-2.01194#1195# Unless required `by applicable law or agreed to in writing, software1196# distributed under the License is distributed on an ""AS-IS"" BASIS,1197# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.1198# See the License for the specific language governing permissions and1199# limitations under the License.1200 

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