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

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Uploaded the version running on the prod server
author george-weingart
date Sun, 08 Feb 2015 23:08:38 -0500
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1 #!/usr/bin/env python
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2 #######################################################################################
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3 # This file is provided under the Creative Commons Attribution 3.0 license.
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4 #
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5 # You are free to share, copy, distribute, transmit, or adapt this work
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6 # PROVIDED THAT you attribute the work to the authors listed below.
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7 # For more information, please see the following web page:
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8 # http://creativecommons.org/licenses/by/3.0/
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9 #
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10 # This file is a component of the SflE Scientific workFLow Environment for reproducible
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11 # research, authored by the Huttenhower lab at the Harvard School of Public Health
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12 # (contact Curtis Huttenhower, chuttenh@hsph.harvard.edu).
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13 #
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14 # If you use this environment, the included scripts, or any related code in your work,
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15 # please let us know, sign up for the SflE user's group (sfle-users@googlegroups.com),
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16 # pass along any issues or feedback, and we'll let you know as soon as a formal citation
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17 # is available.
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18 #######################################################################################
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19
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20 """
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21 Examples
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22 ~~~~~~~~
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23
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24 ``data.pcl``::
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25
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26 a b
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27 c d
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28 e f
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29
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30 ``Examples``::
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31
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32 $ transpose.py < data.pcl
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33 a c e
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34 b d f
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35
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36 $ echo "a b c" | transpose.py
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37 a
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38 b
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39 c
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40
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41 .. testsetup::
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42
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43 from transpose import *
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44 """
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45
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46 import argparse
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47 import csv
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48 import sys
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49
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50 def transpose( aastrIn, ostm ):
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51 """
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52 Outputs the matrix transpose of the input tab-delimited rows.
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53
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54 :param aastrIn: Split lines from which data are read.
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55 :type aastrIn: collection of string collections
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56 :param ostm: Output stream to which transposed rows are written.
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57 :type ostm: output stream
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58
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59 >>> aastrIn = [list(s) for s in ("ab", "cd", "ef")]
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60 >>> transpose( aastrIn, sys.stdout ) #doctest: +NORMALIZE_WHITESPACE
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61 a c e
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62 b d f
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63
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64 >>> transpose( [list("abc")], sys.stdout ) #doctest: +NORMALIZE_WHITESPACE
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65 a
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66 b
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67 c
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68 """
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69
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70 aastrLines = [a for a in aastrIn]
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71 csvw = csv.writer( ostm, csv.excel_tab )
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72 for iRow in range( len( aastrLines[0] ) ):
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73 csvw.writerow( [aastrLines[iCol][iRow] for iCol in range( len( aastrLines ) )] )
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74
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75 argp = argparse.ArgumentParser( prog = "transpose.py",
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76 description = """Transposes a tab-delimited text matrix.
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77
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78 The transposition process is robust to missing elements and rows of differing lengths.""" )
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79 __doc__ = "::\n\n\t" + argp.format_help( ).replace( "\n", "\n\t" ) + __doc__
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80
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81 def _main( ):
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82 args = argp.parse_args( )
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83 transpose( csv.reader( sys.stdin, csv.excel_tab ), sys.stdout )
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84
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85 if __name__ == "__main__":
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86 _main( )