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#!/usr/bin/env python3
#
# Aaron LI
# Created: 2016-06-25
# Updated: 2016-06-26
#
# Change logs:
# 2016-06-26:
# * Allow missing data columns
#
"""
Read a table from a plain text file according to a data column
specification.
The "column" here means the column number by each character.
While the "data column" means a meaningful data which stretch multiple
columns. e.g,
------------------------------------------------------------
1234567890123456789012345678901234567890 -> column
x xxx.xx xxx.x xxxx
xx xx.x xx.xx xxxx
| | | |
DC1 DC2 DC3 DC4 -> data column
------------------------------------------------------------
This table syntax is usually used in optical astronomy, e.g, SDSS tables.
Sample configuration file:
------------------------------------------------------------
## Configuration for `read_table_colspec.py`
## Date: 2016-06-25
# input table file
infile = <INPUT.TXT>
# output file in CSV format
outfile = <OUTPUT.CSV>
# data column specification
# column number is 1-based, and end column is inclusive.
[colspec]
# name = col_begin, col_end, type, comment
ID = 1, 4, int
RA = 5, 15, float, deg
Dec = 16, 26, float, deg
redshift = 27, 34, float
name = 35, -1, str
------------------------------------------------------------
"""
import re
import argparse
import csv
from pydoc import locate
from configobj import ConfigObj
def parse_colspec(config):
"""
Parse the data column specification from the config file.
Parsed colspec syntax:
[
(name, col_begin, col_end, type, comment),
...
]
NOTE: the above `col_begin` and `col_end` are convert to be 0-based.
"""
colspec = []
for name, spec in config.items():
col_begin, col_end = int(spec[0]), int(spec[1])
# Convert column number to be 0-based
col_begin -= 1
if col_end != -1:
col_end -= 1
# Cast from string to type
# Credit: https://stackoverflow.com/a/29831586/4856091
t = locate(spec[2])
if len(spec) == 4:
comment = spec[3]
else:
comment = ""
colspec.append((name, col_begin, col_end, t, comment))
return colspec
def parse_line(line, colspec):
"""
Parse the given line according to the data column specification.
Parse value syntax:
[ (name, value, comment), ... ]
"""
items = []
for name, col_begin, col_end, t, comment in colspec:
if col_end == -1:
value = line[col_begin:].strip()
else:
value = line[col_begin:(col_end+1)].strip()
try:
value = t(value)
except ValueError:
value = None
items.append((name, value, comment))
return items
def main():
parser = argparse.ArgumentParser(
description="Read table data by column specification")
parser.add_argument("config", nargs=1,
help="config of input, output, column specification")
args = parser.parse_args()
config = ConfigObj(args.config[0])
colspec = parse_colspec(config["colspec"])
# output column header
header = [spec[0] if spec[-1] == "" else "%s[%s]" % (spec[0], spec[-1])
for spec in colspec]
with open(config["outfile"], "w") as csv_file:
csv_writer = csv.writer(csv_file)
csv_writer.writerow(header)
# data lines
for line in open(config["infile"]).read().splitlines():
if re.match(r"^\s*$", line):
# ignore blank lines
continue
if re.match(r"^\s*#.*$", line):
continue
#
items = parse_line(line, colspec)
values = [x[1] for x in items]
csv_writer.writerow(values)
if __name__ == "__main__":
main()
|
