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

Uploaded the version running on the prod server

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/maaslin-4450aa4ecc84/transpose.py	Sun Feb 08 23:08:38 2015 -0500
@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+#######################################################################################
+# This file is provided under the Creative Commons Attribution 3.0 license.
+#
+# You are free to share, copy, distribute, transmit, or adapt this work
+# PROVIDED THAT you attribute the work to the authors listed below.
+# For more information, please see the following web page:
+# http://creativecommons.org/licenses/by/3.0/
+#
+# This file is a component of the SflE Scientific workFLow Environment for reproducible 
+# research, authored by the Huttenhower lab at the Harvard School of Public Health
+# (contact Curtis Huttenhower, [e-mail]).
+#
+# If you use this environment, the included scripts, or any related code in your work,
+# please let us know, sign up for the SflE user's group ([e-mail]),
+# pass along any issues or feedback, and we'll let you know as soon as a formal citation
+# is available.
+#######################################################################################
+
+"""
+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( )