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| from __future__ import unicode_literals |
| import sys |
| import os |
| import gzip |
| from tempfile import NamedTemporaryFile |
| from subprocess import Popen, PIPE |
|
|
| if len(sys.argv) < 3 or len(sys.argv) > 4: |
| sys.stderr.write( |
| 'Usage: ' + |
| sys.argv[0] + " in_file out_path [prune_count]\n" |
| "This script will create the files out_path/count-table.gz and " |
| "out_path/count-table-target.gz\n") |
| exit() |
|
|
|
|
| def handle_file(filename, action, fileobj=None, mode='r'): |
| """support reading either from stdin, plain file or gzipped file""" |
|
|
| if action == 'open': |
|
|
| if mode == 'r': |
| mode = 'rb' |
|
|
| if mode == 'rb' and filename != '-' and not os.path.exists(filename): |
| if os.path.exists(filename + '.gz'): |
| filename = filename + '.gz' |
| else: |
| sys.stderr.write( |
| "Error: unable to open file. " + |
| filename + " - aborting.\n") |
| exit() |
|
|
| if filename.endswith('.gz'): |
| fileobj = gzip.open(filename, mode) |
|
|
| elif filename == '-': |
| fileobj = sys.stdin |
|
|
| else: |
| fileobj = open(filename, mode) |
|
|
| return fileobj |
|
|
| elif action == 'close' and filename != '-': |
| fileobj.close() |
|
|
|
|
| def sort_and_uniq(infile, outfile): |
|
|
| cmd = ['sort', infile] |
| fobj = handle_file(outfile, 'open', mode='w') |
| sys.stderr.write( |
| "Executing: LC_ALL=C " + |
| ' '.join(cmd) + |
| ' | uniq | gzip -c > ' + outfile + '\n') |
| p_sort = Popen(cmd, env={'LC_ALL': 'C'}, stdout=PIPE) |
| p_uniq = Popen(['uniq'], stdin=p_sort.stdout, stdout=PIPE) |
| p_compress = Popen(['gzip', '-c'], stdin=p_uniq.stdout, stdout=fobj) |
| p_compress.wait() |
| fobj.close() |
|
|
|
|
| def create_count_lines(fobj, countobj, countobj_target, prune=0): |
|
|
| i = 0 |
| original_pos = 0 |
| source = b"" |
| store_lines = set() |
| for line in fobj: |
|
|
| if not i % 100000: |
| sys.stderr.write('.') |
| i += 1 |
|
|
| line = line.split(b' ||| ') |
| current_source = line[0] |
| scores = line[2].split() |
| comments = line[4].split() |
|
|
| fs = comments[1] |
| ft = comments[0] |
| try: |
| fst = comments[2] |
| except IndexError: |
| fst = str(int(round(float(scores[0]) * float(ft)))).encode() |
|
|
| line[2] = b' '.join([fst, ft, fs]) |
|
|
| if prune: |
| if current_source != source: |
| write_batch(store_lines, countobj, prune) |
| source = current_source |
| store_lines = set() |
| original_pos = 0 |
|
|
| store_lines.add((float(fst), original_pos, b' ||| '.join(line))) |
| original_pos += 1 |
|
|
| else: |
| countobj.write(b' ||| '.join(line)) |
|
|
| |
| |
| |
| tline = b' ||| '.join([line[1], b'X', ft]) + b' ||| |||\n' |
| countobj_target.write(tline) |
|
|
| if prune: |
| write_batch(store_lines, countobj, prune) |
|
|
| countobj.close() |
| countobj_target.close() |
|
|
|
|
| def write_batch(store_lines, outfile, prune): |
| top20 = sorted(store_lines, reverse=True)[:prune] |
| |
| for score, original_pos, store_line in sorted(top20, key=lambda x: x[1]): |
| outfile.write(store_line) |
|
|
|
|
| if __name__ == '__main__': |
|
|
| if len(sys.argv) == 4: |
| prune = int(sys.argv[3]) |
| else: |
| prune = 0 |
|
|
| fileobj = handle_file(sys.argv[1], 'open') |
| out_path = sys.argv[2] |
|
|
| count_table_file = gzip.open( |
| os.path.join(out_path, 'count-table.gz'), 'w') |
| count_table_target_file = os.path.join(out_path, 'count-table-target.gz') |
|
|
| count_table_target_file_temp = NamedTemporaryFile(delete=False) |
| try: |
| sys.stderr.write( |
| "Creating temporary file for unsorted target counts file: " + |
| count_table_target_file_temp.name + '\n') |
|
|
| create_count_lines( |
| fileobj, count_table_file, count_table_target_file_temp, prune) |
| count_table_target_file_temp.close() |
| sys.stderr.write( |
| "Finished writing, " |
| "now re-sorting and compressing target count file.\n") |
|
|
| sort_and_uniq( |
| count_table_target_file_temp. name, count_table_target_file) |
| os.remove(count_table_target_file_temp.name) |
| sys.stderr.write('Done\n') |
|
|
| except BaseException: |
| os.remove(count_table_target_file_temp.name) |
| raise |
|
|