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src/q/i/qiime-1.8.0/scripts/print_qiime_config.py   qiime(Download)
 
try:    
    from cogent.util.misc import app_path, get_random_directory_name, remove_files
    from cogent.app.util import ApplicationNotFoundError, ApplicationError
    from cogent import __version__ as pycogent_lib_version
 
        # remove log file
        remove_files([log_file], error_on_missing = False)
 
        version_string = stdout.strip().split(' ')[1].strip('v.')
 
        # remove log file generated
        remove_files(['ParsInsert.log'], error_on_missing=False)
 
        version_string = stdout.strip()

src/q/i/qiime-1.8.0/qiime/workflow/pick_open_reference_otus.py   qiime(Download)
from numpy import inf
from copy import deepcopy
from cogent.util.misc import create_dir, remove_files
from cogent.parse.fasta import MinimalFastaParser
from qiime.util import (subsample_fasta)
    commands.append([('Build phylogenetic tree', make_phylogeny_cmd)])
    if exists(tree_fp):
        remove_files([tree_fp])
 
    # Call the command handler on the list of commands
        else:
            # remove files from partially completed runs
            remove_files([otu_table_w_tax_fp],error_on_missing=False)
 
            taxonomy_fp = assign_tax(
        else:
            # remove files from partially completed runs
            remove_files([pynast_failure_filtered_otu_table_fp],
                         error_on_missing=False)
 
        else:
            # remove files from partially completed runs
            remove_files([otu_table_w_tax_fp],error_on_missing=False)
 
            taxonomy_fp = assign_tax(

src/q/i/qiime-1.8.0/qiime/identify_chimeric_seqs.py   qiime(Download)
from datetime import datetime
 
from cogent.util.misc import remove_files, app_path
from cogent.parse.fasta import MinimalFastaParser
from cogent.app.formatdb import build_blast_db_from_fasta_path
from cogent.app.parameters import ValuedParameter, FlagParameter
from cogent.app.util import CommandLineApplication, ResultPath,\
    ApplicationError, ApplicationNotFoundError
from cogent.util.misc import remove_files
    def cleanUp(self):
        """ Remove temporary blast database files, if applicable
        """
        remove_files(self._db_files_to_remove,error_on_missing=False)
 
                        ".CPS.CPC.wTaxons", ".cidx"]
        cs_tmp_files = [exec_dir +'/'+ inp_file_name + x for x in tmp_suffixes]
        remove_files(cs_tmp_files, error_on_missing=False)
 
        db_param = self.Parameters['--db_NAST']
 
            blast_db_files = [fasta_name + x for x in [".nsq",".nin",".nhr",".cidx"]]
            remove_files(blast_db_files, error_on_missing=False)
 
    def getHelp(self):

src/q/i/qiime-1.8.0/qiime/pick_otus.py   qiime(Download)
from cogent.app.blast import blast_seqs, Blastall, BlastResult
from cogent.core.sequence import DnaSequence
from cogent.util.misc import remove_files
from cogent import LoadSeqs, DNA, Alignment
from cogent.util.trie import build_prefix_map
            log_file.write('Failures: %s\n' % '\t'.join(failures))
 
        remove_files(self.db_files_to_remove,error_on_missing=False)
        # return the result (note this is None if the data was
        # written to file)
 
        # clean up any temp files that were created
        remove_files(self.files_to_remove)
 
        log_lines = []
 
        # clean up any temp files that were created
        remove_files(self.files_to_remove)
 
        log_lines = []
 
        # clean up any temp files that were created
        remove_files(self.files_to_remove)
 
        log_lines = []

src/p/y/pynast-1.2.2/pynast/util.py   pynast(Download)
 
from cogent import DNA, LoadSeqs, Sequence
from cogent.util.misc import remove_files
from cogent.core.alignment import SequenceCollection, DenseAlignment
from cogent.align.align import make_dna_scoring_dict, global_pairwise
            # clean-up temporary blast database files if any were created
            pw_alignment_iterator.close()
            remove_files(files_to_remove,error_on_missing=False)
            raise ValueError, "Candidate sequence contains gaps. This is not supported."
 
 
    # clean-up temporary blast database files if any were created
    remove_files(files_to_remove,error_on_missing=False)
 
 

src/c/o/cogent-1.5.3/cogent/app/usearch.py   cogent(Download)
from cogent.app.util import CommandLineApplication, ResultPath,\
 get_tmp_filename, ApplicationError, ApplicationNotFoundError
from cogent.util.misc import remove_files
 
from cogent.app.uclust import clusters_from_uc_file
 
    if not save_intermediate_files:
        remove_files([uc_filepath])
 
    # Returning output filepath to delete if specified.
 
    if not save_intermediate_files:
        remove_files([uc_filepath])
 
    # Returning output filepath to delete if specified.
 
    if not save_intermediate_files:
        remove_files([output_chimera_filepath])
 
    return app_result, output_non_chimera_filepath
 
    if not save_intermediate_files:
        remove_files([cluster_filepath, output_chimera_filepath])
 
    return app_result, output_non_chimera_filepath

src/p/y/pycogent-HEAD/cogent/app/usearch.py   pycogent(Download)
from cogent.app.util import CommandLineApplication, ResultPath,\
 get_tmp_filename, ApplicationError, ApplicationNotFoundError
from cogent.util.misc import remove_files
 
from cogent.app.uclust import clusters_from_uc_file
 
    if not save_intermediate_files:
        remove_files([uc_filepath])
 
    # Returning output filepath to delete if specified.
 
    if not save_intermediate_files:
        remove_files([uc_filepath])
 
    # Returning output filepath to delete if specified.
 
    if not save_intermediate_files:
        remove_files([output_chimera_filepath])
 
    return app_result, output_non_chimera_filepath
 
    if not save_intermediate_files:
        remove_files([cluster_filepath, output_chimera_filepath])
 
    return app_result, output_non_chimera_filepath

src/c/o/cogent-1.5.3/cogent/app/uclust.py   cogent(Download)
from cogent.app.util import CommandLineApplication, ResultPath,\
 get_tmp_filename, ApplicationError, ApplicationNotFoundError
from cogent.util.misc import remove_files
from cogent import DNA
 
         HALT_EXEC=HALT_EXEC)
        # Get cluster file name from application wrapper
        remove_files(files_to_remove)
    except ApplicationError:
        remove_files(files_to_remove)
        raise ApplicationError, ('Error running uclust. Possible causes are '
         'unsupported version (current supported version is v1.2.22) is installed or '
         'improperly formatted input file was provided')
    except ApplicationNotFoundError:
        remove_files(files_to_remove)

src/p/y/pycogent-HEAD/cogent/app/uclust.py   pycogent(Download)
from cogent.app.util import CommandLineApplication, ResultPath,\
 get_tmp_filename, ApplicationError, ApplicationNotFoundError
from cogent.util.misc import remove_files
from cogent import DNA
 
         HALT_EXEC=HALT_EXEC)
        # Get cluster file name from application wrapper
        remove_files(files_to_remove)
    except ApplicationError:
        remove_files(files_to_remove)
        raise ApplicationError, ('Error running uclust. Possible causes are '
         'unsupported version (current supported version is v1.2.22) is installed or '
         'improperly formatted input file was provided')
    except ApplicationNotFoundError:
        remove_files(files_to_remove)

src/q/i/qiime-1.8.0/qiime/pycogent_backports/usearch.py   qiime(Download)
from cogent.app.util import CommandLineApplication, ResultPath,\
 get_tmp_filename, ApplicationError, ApplicationNotFoundError
from cogent.util.misc import remove_files
from qiime.pycogent_backports.uclust import clusters_from_uc_file
 
 
    if not save_intermediate_files:
        remove_files([uc_filepath])
 
    # Returning output filepath to delete if specified.
 
    if not save_intermediate_files:
        remove_files([uc_filepath])
 
    # Returning output filepath to delete if specified.
 
    if not save_intermediate_files:
        remove_files([output_chimera_filepath])
 
    return app_result, output_non_chimera_filepath
 
    if not save_intermediate_files:
        remove_files([cluster_filepath, output_chimera_filepath])
 
    return app_result, output_non_chimera_filepath

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