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src/q/i/qiime-1.8.0/scripts/denoiser.py   qiime(Download)
 
from qiime.util import get_tmp_filename
from cogent.util.misc import create_dir
 
from qiime.util import parse_command_line_parameters, get_options_lookup,\
        tmpoutdir = get_tmp_filename(tmp_dir="", prefix="denoiser_", suffix="/")
 
    create_dir(tmpoutdir, not opts.force)
 
    log_fp = 'denoiser.log'

src/q/i/qiime-1.8.0/qiime/denoiser/make_cluster_jobs.py   qiime(Download)
from subprocess import Popen, PIPE, STDOUT
 
from cogent.util.misc import app_path, create_dir
from cogent.app.util import ApplicationNotFoundError
from qiime.util import get_tmp_filename
 
    filenames=[]
    create_dir(jobs_dir)
    for command in commands:
        job_name = get_tmp_filename(tmp_dir=jobs_dir, prefix=job_prefix+"_",

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)
         and handle processing of the results.
    """
    create_dir(output_dir)
    commands = []
    if logger == None:
    input_dir, input_filename = split(input_fp)
    input_basename, input_ext = splitext(input_filename)
    create_dir(output_dir)
    commands = []
    if logger == None:
    if step1_otu_map_fp and step1_failures_fasta_fp:
        step1_dir = '%s/step1_otus' % output_dir
        create_dir(step1_dir)
        logger.write("Using pre-existing reference otu map and failures.\n\n")
    else:

src/q/i/qiime-1.8.0/qiime/parallel/beta_diversity.py   qiime(Download)
 
from os.path import join, split, splitext
from cogent.util.misc import create_dir
from biom.parse import parse_biom_table
from qiime.parallel.util import ParallelWrapper
        for i, sample_id_group in enumerate(sample_id_groups):
            working_dir_i = join(working_dir, str(i))
            create_dir(working_dir_i)
            output_dir_i = join(output_dir, str(i))
            create_dir(output_dir_i)

src/q/i/qiime-1.8.0/qiime/util.py   qiime(Download)
    build_blast_db_from_fasta_file
from cogent import LoadSeqs
from cogent.util.misc import (create_dir, 
                              handle_error_codes)
 
        when working with large numbers of samples ids (e.g. > 1024 on linux)
    """
    create_dir(output_dir)
    file_lookup = {}
    all_fps = []

src/q/i/qiime-1.8.0/qiime/denoiser/utils.py   qiime(Download)
 
from cogent.app.util import ApplicationNotFoundError,ApplicationError
from cogent.util.misc import app_path, create_dir
from cogent.parse.flowgram_parser import lazy_parse_sff_handle
from qiime.util import (get_qiime_project_dir, get_qiime_scripts_dir,
    checkpoint_dir = out_fp+"/checkpoints/"
    if (not exists(checkpoint_dir)):
        create_dir(checkpoint_dir)
    out_fp = checkpoint_dir+"/checkpoint%d.pickle" % ctr
    out_fh = open(out_fp, "w")

src/q/i/qiime-1.8.0/qiime/stats.py   qiime(Download)
from numpy import argsort, min as np_min, max as np_max, log10
from numpy.random import permutation
from cogent.util.misc import combinate, create_dir
from cogent.maths.stats.test import t_one_sample
 
 
    # create the output directory if it doesn't already exist
    create_dir(output_dir)
 
    num_analysis_categories = len(analysis_categories)

src/q/i/qiime-1.8.0/scripts/split_libraries_fastq.py   qiime(Download)
 
from cogent import DNA
from cogent.util.misc import safe_md5, create_dir
from qiime.util import parse_command_line_parameters, make_option, gzip_open
from qiime.parse import parse_mapping_file
 
    output_dir = opts.output_dir
    create_dir(output_dir)
 
    output_fp_temp = '%s/seqs.fna.incomplete' % output_dir

src/q/i/qiime-1.8.0/scripts/process_qseq.py   qiime(Download)
from glob import glob
from os.path import split
from cogent.util.misc import create_dir
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.format import illumina_data_to_fastq
    input_dir = opts.input_dir
    output_dir = opts.output_dir
    create_dir(output_dir)
    lanes = opts.lanes.split(',')
    bases = opts.bases

src/q/i/qiime-1.8.0/scripts/process_iseq.py   qiime(Download)
from glob import glob
from os.path import split, splitext
from cogent.util.misc import create_dir
from qiime.util import (parse_command_line_parameters, make_option,
                        iseq_to_qseq_fields, gzip_open)
    input_fps = opts.input_fps
    output_dir = opts.output_dir
    create_dir(output_dir)
    barcode_length = opts.barcode_length
    barcode_in_header = opts.barcode_in_header

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