annotate maaslin-4450aa4ecc84/src/transpose.py @ 1:a87d5a5f2776

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#!/usr/bin/env python
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"""
Examples
~~~~~~~~

``data.pcl``::

	a	b
	c	d
	e	f

``Examples``::

	$ transpose.py < data.pcl
	a	c	e
	b	d	f

	$ echo "a	b	c" | transpose.py
	a
	b
	c

.. testsetup::

	from transpose import *
"""

import argparse
import csv
import sys

def transpose( aastrIn, ostm ):
	"""
	Outputs the matrix transpose of the input tab-delimited rows. 
	
	:param	aastrIn:	Split lines from which data are read.
	:type	aastrIn:	collection of string collections
	:param	ostm:		Output stream to which transposed rows are written.
	:type	ostm:		output stream

	>>> aastrIn = [list(s) for s in ("ab", "cd", "ef")]
	>>> transpose( aastrIn, sys.stdout ) #doctest: +NORMALIZE_WHITESPACE
	a	c	e
	b	d	f
	
	>>> transpose( [list("abc")], sys.stdout ) #doctest: +NORMALIZE_WHITESPACE
	a
	b
	c
	"""

	aastrLines = [a for a in aastrIn]
	csvw = csv.writer( ostm, csv.excel_tab )
	for iRow in range( len( aastrLines[0] ) ):
		csvw.writerow( [aastrLines[iCol][iRow] for iCol in range( len( aastrLines ) )] )

argp = argparse.ArgumentParser( prog = "transpose.py",
	description = """Transposes a tab-delimited text matrix.

The transposition process is robust to missing elements and rows of differing lengths.""" )
__doc__ = "::\n\n\t" + argp.format_help( ).replace( "\n", "\n\t" ) + __doc__

def _main( ):
	args = argp.parse_args( )
	transpose( csv.reader( sys.stdin, csv.excel_tab ), sys.stdout )

if __name__ == "__main__":
	_main( )