Python FileHandlers.search_directory方法代码示例

本文整理汇总了Python中util.FileHandlers.search_directory方法的典型用法代码示例。如果您正苦于以下问题：Python FileHandlers.search_directory方法的具体用法？Python FileHandlers.search_directory怎么用？Python FileHandlers.search_directory使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类util.FileHandlers的用法示例。

在下文中一共展示了FileHandlers.search_directory方法的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: init

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
 def __init__(self, pdb_code, sequence_annotations, SurfRes=False,
              pocket=False, lpocket=False):
     self.filename = pdb_code
     self.sequence_annotations = sequence_annotations
     if SurfRes:
         file_handlers = FileHandlers()
         file_paths = file_handlers.search_directory()
         txt_files = file_handlers.find_files(file_paths, 'txt')
         for txt_file in txt_files:
             if (self.filename + '_SurfRes.txt') == \
                     file_handlers.get_file_name(txt_file):
                 self.surfres_file = txt_file
             else:
                 self.surfres_file = ''
     if pocket:
         file_handlers = FileHandlers()
         file_paths = file_handlers.search_directory()
         txt_files = file_handlers.find_files(file_paths, 'txt')
         for txt_file in txt_files:
             if (self.filename + '_pocketres.txt') == \
                     file_handlers.get_file_name(txt_file):
                 self.pocketres_file = txt_file
             else:
                 self.pocketres_file = ''
     if lpocket:
         file_handlers = FileHandlers()
         file_paths = file_handlers.search_directory()
         txt_files = file_handlers.find_files(file_paths, 'txt')
         for txt_file in txt_files:
             if (self.filename + '_lpocket.txt') == \
                     file_handlers.get_file_name(txt_file):
                 self.lpocket_file = txt_file
             else:
                 self.lpocket_file = ''

开发者ID:kata9238，项目名称:bioverse，代码行数:36，代码来源:highlight_targets.py

示例2: main

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
def main():
	file_handlers = FileHandlers()
	file_paths = file_handlers.search_directory()
	fasta_files = file_handlers.find_files(file_paths, 'fasta')
	for path in fasta_files:
		file_name, file_list, interval = find_indices(path)
		write_fasta_new_names(path, file_name, file_list, interval)

开发者ID:AndreaEdwards，项目名称:CAZy_phylogenetics，代码行数:9，代码来源:analysis_v4.py

示例3: init

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
class PickleFasta:
	def __init__(self):
		self.file_handlers = FileHandlers()

	def _get_fasta_files(self):
		file_paths = self.file_handlers.search_directory()
		fasta_files = self.file_handlers.find_files(file_paths, 'faa')
		print "There are %d .faa files in this directory" % len(fasta_files)
		return fasta_files

	def pickle_organism_fasta(self):
		fasta_files = self._get_fasta_files()
		fasta_dictionary = {}
		for fasta_file in fasta_files:
			file_name = self.file_handlers.get_file_name(fasta_file)
			name_list = file_name.split('.')
			Data = open(fasta_file)
			D = Data.readlines()
			Data.close()
			for d in D:
				if d.startswith('>'):
					d_list = d.split(' ')
					if name_list[0] in fasta_dictionary:
						fasta_dictionary[name_list[0]].append(d_list[0].lstrip('>'))
					else:
						fasta_dictionary[name_list[0]] = [d_list[0].lstrip('>')]
				else:
					pass
		return fasta_dictionary

开发者ID:AndreaEdwards，项目名称:phylogenetics_analysis_tools，代码行数:31，代码来源:fix_names.py

示例4: _get_pdb_file_path

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
	def _get_pdb_file_path(self):
		file_handlers = FileHandlers()
		file_paths = file_handlers.search_directory()
		pdb_files = file_handlers.find_files(file_paths, 'pdb')
		for pdb_file in pdb_files:
			if (self.filename + '_0001') == file_handlers.get_file_name(pdb_file).split('.')[0]:
				self.file_path = pdb_file

开发者ID:AndreaEdwards，项目名称:design_pipeline，代码行数:9，代码来源:seq.py

示例5: _get_outfile

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
 def _get_outfile(self):
     file_handlers = FileHandlers()
     file_paths = file_handlers.search_directory()
     out_files = file_handlers.find_files(file_paths, 'out')
     if (self.pdb_code != '' and self.psiblast != ''):
         for out_file in out_files:
             if (self.pdb_code + '_mutants') == \
                     file_handlers.get_file_name(out_file).split('.')[0]:
                 self.ddG_results_filepath = out_file
             elif (self.psiblast + '_mutants') == \
                     file_handlers.get_file_name(out_file).split('.')[0]:
                 self.llikelihood_filepath = out_file
     elif (self.pdb_code != '' and self.psiblast == ''):
         for out_file in out_files:
             if (self.pdb_code + '_mutants') == \
                     file_handlers.get_file_name(out_file).split('.')[0]:
                 self.ddG_results_filepath = out_file
                 print "Fetching data from %s ....." % \
                     file_handlers.get_file_name(out_file)
     elif (self.pdb_code == '' and self.psiblast != ''):
         for out_file in out_files:
             if (self.psiblast + '_mutants') == \
                     file_handlers.get_file_name(out_file).split('.')[0]:
                 self.llikelihood_filepath = out_file
     else:
         print "You have not specified any results data to parse."
         exit(1)

开发者ID:kata9238，项目名称:bioverse，代码行数:29，代码来源:seq.py

示例6: main

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
def main():
    file_handlers = FileHandlers()
    file_paths = file_handlers.search_directory()
    pep_files = file_handlers.find_files(file_paths, "pep")
    for pep_file in pep_files:
        file_name = file_handlers.get_file_name(pep_file)
        run_muscle(pep_file, file_name)

开发者ID:AndreaEdwards，项目名称:phylogenetics_analysis_tools，代码行数:9，代码来源:run_muscle.py

示例7: _get_downloaded_file_path

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
	def _get_downloaded_file_path(self, pdb_code):
		file_handlers = FileHandlers()
		file_paths = file_handlers.search_directory()
		ent_files = file_handlers.find_files(file_paths, 'ent')
		for ent_file in ent_files:
			if pdb_code == file_handlers.get_file_name(ent_file).split('.')[0].lstrip('pdb').upper():
				return ent_file

开发者ID:cierrajanewalker，项目名称:design_pipeline，代码行数:9，代码来源:pdb.py

示例8: main

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
def main():
	file_handlers = FileHandlers()
	file_paths = file_handlers.search_directory()
	fasta_files = file_handlers.find_files(file_paths, 'fasta')
	for path in fasta_files:
		file_name = file_handlers.get_file_name(path)
		get_dm_raxml(path, file_name, 4)

开发者ID:AndreaEdwards，项目名称:phylogenetics_analysis_tools，代码行数:9，代码来源:run_raxml_dm_calulator.py

示例9: _get_pdb

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
	def _get_pdb(self):
		#os.chdir("./database/pdbs/pdb")
		file_handlers = FileHandlers()
		file_paths = file_handlers.search_directory()
		pdb_files = file_handlers.find_files(file_paths, 'pdb')
		for pdb_file in pdb_files:
			if self.filename == file_handlers.get_file_name(pdb_file).split('.')[0]:
				PDB = open(pdb_file)
				self.pdb = PDB.readlines()
				PDB.close()

开发者ID:cierrajanewalker，项目名称:design_pipeline，代码行数:12，代码来源:pdb.py

示例10: _get_file_path

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
	def _get_file_path(self):
		os.chdir("./database/pdbs/pdb")
		file_handlers = FileHandlers()
		file_paths = file_handlers.search_directory()
		pdb_files = file_handlers.find_files(file_paths, 'pdb')
		for pdb_file in pdb_files:
			if (self.filename + '_0001') == file_handlers.get_file_name(pdb_file).split('.')[0]:
				self.file_path = pdb_file
				self.out_file = file_handlers.get_file_name(pdb_file).split('.')[0] + '_pops.out'
				self.out_file_path = self.dir_path + '/' + self.out_file

开发者ID:cierrajanewalker，项目名称:design_pipeline，代码行数:12，代码来源:pdb.py

示例11: _get_output

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
	def _get_output(self):
		file_handlers = FileHandlers()
		file_paths = file_handlers.search_directory()
		out_files = file_handlers.find_files(file_paths, 'out')
		for out_file in out_files:
			TXT = open(out_file)
			data = TXT.readlines()
			TXT.close()
		os.remove(out_file)
		return data

开发者ID:cierrajanewalker，项目名称:design_pipeline，代码行数:12，代码来源:pdb.py

示例12: _get_data

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
	def _get_data(self, filename):
		file_handlers = FileHandlers()
		file_paths = file_handlers.search_directory()
		txt_files = file_handlers.find_files(file_paths, 'txt')
		for txt_file in txt_files:
			if filename == file_handlers.get_file_name(txt_file):
				TXT = open(txt_file)
				data = TXT.readlines()
				TXT.close()
		return data

开发者ID:AndreaEdwards，项目名称:design_pipeline，代码行数:12，代码来源:stats.py

示例13: _get_data

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
	def _get_data(self, file_tag):
		file_handlers = FileHandlers()
		file_paths = file_handlers.search_directory()
		txt_files = file_handlers.find_files(file_paths, 'txt')
		for txt_file in txt_files:
			if self.filename == file_handlers.get_file_name(txt_file).split('_')[0]:
				if (file_tag.split('_')[1] + '.txt') == file_handlers.get_file_name(txt_file).split('_')[1]:
					TXT = open(txt_file)
					self.data = TXT.readlines()
					TXT.close()

开发者ID:cierrajanewalker，项目名称:design_pipeline，代码行数:12，代码来源:pdb.py

示例14: _open_file

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
	def _open_file(self):
		#os.chdir("../src/database/pdbs")
		file_handlers = FileHandlers()
		file_paths = file_handlers.search_directory()
		pdb_files = file_handlers.find_files(file_paths, 'pdb')
		for pdb_file in pdb_files:
			if self.filename == file_handlers.get_file_name(pdb_file).split('.')[0]:
				Data = open(pdb_file)
				self.data = Data.readlines()
				Data.close

开发者ID:Hockstad，项目名称:design_pipeline，代码行数:12，代码来源:pdb.py

示例15: _get_filename

# 需要导入模块: from util import FileHandlers [as 别名]
# 或者: from util.FileHandlers import search_directory [as 别名]
 def _get_filename(self):
     file_handlers = FileHandlers()
     file_paths = file_handlers.search_directory()
     pdb_files = file_handlers.find_files(file_paths, "pdb")
     if self.tag == "":
         for pdb_file in pdb_files:
             if self.filename == file_handlers.get_file_name(pdb_file).split(".")[0]:
                 return file_handlers.get_file_name(pdb_file).split(".")[0]
     else:
         for pdb_file in pdb_files:
             if (self.filename + self.tag) == file_handlers.get_file_name(pdb_file).split(".")[0]:
                 return file_handlers.get_file_name(pdb_file).split(".")[0]

开发者ID:kata9238，项目名称:bioverse，代码行数:14，代码来源:jmol_spt_writer.py

注：本文中的util.FileHandlers.search_directory方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。

示例1: __init__

示例2: main

示例3: __init__

示例4: _get_pdb_file_path

示例5: _get_outfile

示例6: main

示例7: _get_downloaded_file_path

示例8: main

示例9: _get_pdb

示例10: _get_file_path

示例11: _get_output

示例12: _get_data

示例13: _get_data

示例14: _open_file

示例15: _get_filename

示例1: init

示例3: init