<commit_before>
from __future__ import print_function
from __future__ import division

import numpy as np
import scipy as sp
import pdb
import h5py
import sys
import argparse
import logging
import time
import gzip
import re
import os
import math
import uuid
import socket
from collections import defaultdict
from datetime import datetime

verboseprint=lambda *a, **k: None
__version__ = "1.0"


def main():

    parser=argparse.ArgumentParser(description='Extract c-data from HDF5 file into TXT (matrix.gz)',formatter_class=argparse.ArgumentDefaultsHelpFormatter)

    parser.add_argument('-i', '--input', dest='in_file', type=str, required=True, help='interaction matrix hdf5 file')
    parser.add_argument('-v', '--verbose', dest='verbose',  action='count', help='Increase verbosity (specify multiple times for more)')
    parser.add_argument('--info',dest='info', action='store_true', help='interaction matrix hdf5 file')
    parser.add_argument('-o', '--output', dest='out_file', type=str, help='interaction matrix output file')
    parser.add_argument('-wm', dest='write_mode', default='all', choices=['cis','seperate','all'], help='write mode (cis=cis only maps, seperate=all cis/trans seperate fiels, all=single matrix)')
    parser.add_argument('-z', '--zoom', dest='zoom_coords', nargs='+', type=str, default=[], help='x/y axis zoom coordinate')
    parser.add_argument('-xz', '--xzoom', dest='x_zoom_coords', nargs='+', type=str, default=[], help='x axis zoom coordinate')
    parser.add_argument('-yz', '--yzoom', dest='y_zoom_coords', nargs='+', type=str, default=[], help='y axis zoom coordinate')
    parser.add_argument('-e', '--elements', dest='bed_file', nargs='+', type=str, default=[], help='x/y axis elements bed file (bed3+ format)')
    parser.add_argument('-xe', '--xelements', dest='x_bed_file', nargs='+', type=str, default=[], help='x axis elements bed file (bed3+ format)')
    parser.add_argument('-ye', '--yelements', dest='y_bed_file', nargs='+', type=str, default=[], help='y axis elements bed file (bed3+ format)')
    parser.add_argument('--element_exten', dest='element_exten', type=int, default=0, help='bp extension for all elements, +/- bp to start/end of each element')
    parser.add_argument('-c','--chrs', dest='selected_chrs', nargs='+', type=str, default=[], help='x/y axis subset of chromosomes to extract')
    parser.add_argument('-xc','--xchrs', dest='x_selected_chrs', nargs='+', type=str, default=[], help='x axis subset of chromosomes to extract')
    parser.add_argument('-yc','--ychrs', dest='y_selected_chrs', nargs='+', type=str, default=[], help='y axis subset of chromosomes to extract')
    parser.add_argument('-b','--blocksize', dest='blocksize', type=int, default=None, help='block size of HDF5 file')
    parser.add_argument('-p', dest='precision', type=int, default=4, help='output precision (# of digits)')
    parser.add_argument('--maxdim', dest='max_dimension', type=int, default=12000 , help='maximum dimension of allxall matrix - else cis only')
    parser.add_argument('--outputbins', dest='output_bins',  action='store_true', help='output the bin position file, no matrix output')
    parser.add_argument('--outputfactors', dest='output_factors', action='store_true', help='output the balancing factor list file, no matrix output')
    parser.add_argument('--version', action='version', version='%(prog)s'+__version__)
    
    args=parser.parse_args()

    in_file=args.in_file
    verbose=args.verbose
    info=args.info
    out_file=args.out_file
    write_mode=args.write_mode
    zoom_coords=args.zoom_coords
    x_zoom_coords=args.x_zoom_coords
    y_zoom_coords=args.y_zoom_coords
    bed_file=args.bed_file<commit_msg>formatting error for version<commit_after>
from __future__ import print_function
from __future__ import division

import numpy as np
import scipy as sp
import pdb
import h5py
import sys
import argparse
import logging
import time
import gzip
import re
import os
import math
import uuid
import socket
from collections import defaultdict
from datetime import datetime

verboseprint=lambda *a, **k: None
__version__ = "1.0"


def main():

    parser=argparse.ArgumentParser(description='Extract c-data from HDF5 file into TXT (matrix.gz)',formatter_class=argparse.ArgumentDefaultsHelpFormatter)

    parser.add_argument('-i', '--input', dest='in_file', type=str, required=True, help='interaction matrix hdf5 file')
    parser.add_argument('-v', '--verbose', dest='verbose',  action='count', help='Increase verbosity (specify multiple times for more)')
    parser.add_argument('--info',dest='info', action='store_true', help='interaction matrix hdf5 file')
    parser.add_argument('-o', '--output', dest='out_file', type=str, help='interaction matrix output file')
    parser.add_argument('-wm', dest='write_mode', default='all', choices=['cis','seperate','all'], help='write mode (cis=cis only maps, seperate=all cis/trans seperate fiels, all=single matrix)')
    parser.add_argument('-z', '--zoom', dest='zoom_coords', nargs='+', type=str, default=[], help='x/y axis zoom coordinate')
    parser.add_argument('-xz', '--xzoom', dest='x_zoom_coords', nargs='+', type=str, default=[], help='x axis zoom coordinate')
    parser.add_argument('-yz', '--yzoom', dest='y_zoom_coords', nargs='+', type=str, default=[], help='y axis zoom coordinate')
    parser.add_argument('-e', '--elements', dest='bed_file', nargs='+', type=str, default=[], help='x/y axis elements bed file (bed3+ format)')
    parser.add_argument('-xe', '--xelements', dest='x_bed_file', nargs='+', type=str, default=[], help='x axis elements bed file (bed3+ format)')
    parser.add_argument('-ye', '--yelements', dest='y_bed_file', nargs='+', type=str, default=[], help='y axis elements bed file (bed3+ format)')
    parser.add_argument('--element_exten', dest='element_exten', type=int, default=0, help='bp extension for all elements, +/- bp to start/end of each element')
    parser.add_argument('-c','--chrs', dest='selected_chrs', nargs='+', type=str, default=[], help='x/y axis subset of chromosomes to extract')
    parser.add_argument('-xc','--xchrs', dest='x_selected_chrs', nargs='+', type=str, default=[], help='x axis subset of chromosomes to extract')
    parser.add_argument('-yc','--ychrs', dest='y_selected_chrs', nargs='+', type=str, default=[], help='y axis subset of chromosomes to extract')
    parser.add_argument('-b','--blocksize', dest='blocksize', type=int, default=None, help='block size of HDF5 file')
    parser.add_argument('-p', dest='precision', type=int, default=4, help='output precision (# of digits)')
    parser.add_argument('--maxdim', dest='max_dimension', type=int, default=12000 , help='maximum dimension of allxall matrix - else cis only')
    parser.add_argument('--outputbins', dest='output_bins',  action='store_true', help='output the bin position file, no matrix output')
    parser.add_argument('--outputfactors', dest='output_factors', action='store_true', help='output the balancing factor list file, no matrix output')
    parser.add_argument('--version', action='version', version='%(prog)s '+__version__)
    
    args=parser.parse_args()

    in_file=args.in_file
    verbose=args.verbose
    info=args.info
    out_file=args.out_file
    write_mode=args.write_mode
    zoom_coords=args.zoom_coords
    x_zoom_coords=args.x_zoom_coords
    y_zoom_coords=args.y_zoom_coords
    bed_file=args.bed_file
{'fraction_non_alphanumeric': 0.1638768898488121, 'fraction_numerical': 0.00458963282937365, 'mean_word_length': 5.8034894398530765, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3579856', 'n_tokens_mistral': 2396, 'n_tokens_neox': 2314, 'n_words': 601}