comparison cwpair2.py @ 9:6469dda597d6 draft

Uploaded

8:1fc26b8e618d

matched pairs are mode, closest, largest or all, where the analysis is run for each method

Input: list of one or more gff format files

Output: files produced for each input/mode combination:
S (simple), D (detailed), O (orphans), P (frequency preview plot), F (final frequency plot),
C (statistics graph), statistics.tabular
"""

import argparse
import csv

    parser.add_argument('--down_distance', dest='down_distance', type=int, default=100, help='Distance downstream of a pair.')
    parser.add_argument('--binsize', dest='binsize', type=int, default=1, help='Width of bins for plots and mode.')
    parser.add_argument('--threshold_format', dest='threshold_format', help='Percentage to filter the 95th percentile.')
    parser.add_argument('--relative_threshold', dest='relative_threshold', type=float, default=0.0, help='Percentage to filter the 95th percentile.')
    parser.add_argument('--absolute_threshold', dest='absolute_threshold', type=float, default=0.0, help='Absolute value to filter.')
    parser.add_argument('--output_files', dest='output_files', default='simple', help='Restrict output dataset collections.')
    parser.add_argument('--sort_score', dest='sort_score', default='no', help='Sort output by score.')
    parser.add_argument('--statistics_output', dest='statistics_output', help='Statistics output file.')
    args = parser.parse_args()

    cwpair2_util.create_directories(args.method)

    statistics = []
    if args.absolute_threshold > 0:
        threshold = args.absolute_threshold
    elif args.relative_threshold > 0:

                                          args.method,
                                          threshold,
                                          args.up_distance,
                                          args.down_distance,
                                          args.binsize,
                                          args.output_files,
                                          args.sort_score)
        statistics.extend(stats)
    # Accumulate statistics.
    by_file = {}
    for stats in statistics:
        # Skip "None" statistics from failed files

9:6469dda597d6

matched pairs are mode, closest, largest or all, where the analysis is run for each method

Input: list of one or more gff format files

Output: files produced for each input/mode combination:
MP (matched_pair), D (details), O (orphans), P (frequency preview plot), F (frequency final plot),
C (statistics graph), statistics.tabular
"""

import argparse
import csv

    parser.add_argument('--down_distance', dest='down_distance', type=int, default=100, help='Distance downstream of a pair.')
    parser.add_argument('--binsize', dest='binsize', type=int, default=1, help='Width of bins for plots and mode.')
    parser.add_argument('--threshold_format', dest='threshold_format', help='Percentage to filter the 95th percentile.')
    parser.add_argument('--relative_threshold', dest='relative_threshold', type=float, default=0.0, help='Percentage to filter the 95th percentile.')
    parser.add_argument('--absolute_threshold', dest='absolute_threshold', type=float, default=0.0, help='Absolute value to filter.')
    parser.add_argument('--output_files', dest='output_files', default='matched_pair', help='Restrict output dataset collections.')
    parser.add_argument('--statistics_output', dest='statistics_output', help='Statistics output file.')
    args = parser.parse_args()

    cwpair2_util.create_directories()

    statistics = []
    if args.absolute_threshold > 0:
        threshold = args.absolute_threshold
    elif args.relative_threshold > 0:

                                          args.method,
                                          threshold,
                                          args.up_distance,
                                          args.down_distance,
                                          args.binsize,
                                          args.output_files)
        statistics.extend(stats)
    # Accumulate statistics.
    by_file = {}
    for stats in statistics:
        # Skip "None" statistics from failed files