parent
598ab102b3
commit
7c735e33f7
@ -1,133 +0,0 @@
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class Writer:
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@staticmethod
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def other_params(args):
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return (args.multiple_output, int(args.sort_by), args.sort_reversed)
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@staticmethod
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def make_output_writer(args, colocation_ids, word_renderer):
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params = Writer.other_params(args)
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return Writer(args.out, OutFormatter(colocation_ids, word_renderer), params)
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@staticmethod
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def make_output_no_stat_writer(args, colocation_ids, word_renderer):
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params = Writer.other_params(args)
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return Writer(args.out_no_stat, OutNoStatFormatter(colocation_ids, word_renderer), params)
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@staticmethod
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def make_all_writer(args, colocation_ids, word_renderer):
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return Writer(args.all, AllFormatter(colocation_ids, word_renderer), None)
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@staticmethod
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def make_stats_writer(args, colocation_ids, word_renderer):
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params = Writer.other_params(args)
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return Writer(args.stats, StatsFormatter(colocation_ids, word_renderer), params)
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def __init__(self, file_out, formatter, params):
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if params is None:
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self.multiple_output = False
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self.sort_by = -1
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self.sort_order = None
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else:
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self.multiple_output = params[0]
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self.sort_by = params[1]
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self.sort_order = params[2]
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self.output_file = file_out
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self.formatter = formatter
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def header(self):
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repeating_cols = self.formatter.header_repeat()
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cols = ["C{}_{}".format(i + 1, thd) for i in range(MAX_NUM_COMPONENTS)
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for thd in repeating_cols]
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cols = ["Structure_ID"] + cols + ["Colocation_ID"]
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cols += self.formatter.header_right()
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return cols
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def sorted_rows(self, rows):
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if self.sort_by < 0 or len(rows) < 2:
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return rows
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if len(rows[0]) <= self.sort_by:
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logging.warning("Cannot sort by column #{}: Not enough columns!".format(len(rows[0])))
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return rows
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try:
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int(rows[0][self.sort_by])
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def key(row):
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return int(row[self.sort_by])
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except ValueError:
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def key(row):
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return row[self.sort_by].lower()
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return sorted(rows, key=key, reverse=self.sort_order)
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def write_header(self, file_handler):
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file_handler.write(", ".join(self.header()) + "\n")
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def write_out_worker(self, file_handler, structure, colocation_ids):
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rows = []
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components = structure.components
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for match in colocation_ids.get_matches_for(structure):
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self.formatter.new_match(match)
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for words in match.matches:
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to_write = []
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for idx, _comp in enumerate(components):
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idx = str(idx + 1)
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if idx not in words:
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to_write.extend([""] * self.formatter.length())
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else:
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to_write.extend(self.formatter.content_repeat(words, match.representations, idx, structure.id))
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# make them equal size
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to_write.extend([""] * (MAX_NUM_COMPONENTS * self.formatter.length() - len(to_write)))
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# structure_id and colocation_id
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to_write = [structure.id] + to_write + [match.match_id]
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# header_right
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to_write.extend(self.formatter.content_right(len(match)))
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rows.append(to_write)
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if self.formatter.group():
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break
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if rows != []:
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rows = self.sorted_rows(rows)
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file_handler.write("\n".join([", ".join(row) for row in rows]) + "\n")
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file_handler.flush()
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def write_out(self, structures, colocation_ids):
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if self.output_file is None:
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return
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def fp_close(fp_):
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if fp_ != sys.stdout:
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fp_.close()
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def fp_open(snum=None):
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if snum is None:
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return open(self.output_file, "w")
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else:
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return open("{}.{}".format(self.output_file, snum), "w")
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if not self.multiple_output:
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fp = fp_open()
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self.write_header(fp)
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for s in structures:
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if self.multiple_output:
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fp = fp_open(s.id)
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self.write_header(fp)
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self.formatter.set_structure(s)
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self.write_out_worker(fp, s, colocation_ids)
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if self.multiple_output:
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fp_close(fp)
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if not self.multiple_output:
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fp_close(fp)
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