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1 """
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2 Sorts tabular data on one or more columns.
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3
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4 usage: %prog [options]
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5 -i, --input=i: Tabular file to be sorted
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6 -o, --out_file1=o: Sorted output file
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7 -c, --column=c: First column to sort on
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8 -s, --style=s: Sort style (numerical or alphabetical)
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9 -r, --order=r: Order (ASC or DESC)
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10
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11 usage: %prog input out_file1 column style order [column style ...]
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12 """
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13
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14 import os, re, string, sys
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15 from galaxy import eggs
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16 import pkg_resources; pkg_resources.require( "bx-python" )
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17 from bx.cookbook import doc_optparse
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18
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19 def stop_err( msg ):
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20 sys.stderr.write( "%s\n" % msg )
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21 sys.exit()
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22
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23 def main():
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24 #Parse Command Line
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25 options, args = doc_optparse.parse( __doc__ )
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26 try:
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27 inputfile = options.input
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28 outputfile = '-o %s' % options.out_file1
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29 columns = [options.column]
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30 styles = [('','n')[options.style == 'num']]
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31 orders = [('','r')[options.order == 'DESC']]
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32 col_style_orders = sys.argv[6:]
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33 if len(col_style_orders) > 1:
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34 columns.extend([col_style_orders[i] for i in range(0,len(col_style_orders),3)])
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35 styles.extend([('','n')[col_style_orders[i] == 'num'] for i in range(1,len(col_style_orders),3)])
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36 orders.extend([('','r')[col_style_orders[i] == 'DESC'] for i in range(2,len(col_style_orders),3)])
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37 cols = [ '-k%s,%s%s%s'%(columns[i], columns[i], styles[i], orders[i]) for i in range(len(columns)) ]
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38 except Exception, ex:
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39 stop_err('Error parsing input parameters\n' + str(ex))
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40
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41 # Launch sort.
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42 cmd = "sort -f -t ' ' %s %s %s" % (' '.join(cols), outputfile, inputfile)
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43 try:
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44 os.system(cmd)
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45 except Exception, ex:
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46 stop_err('Error running sort command\n' + str(ex))
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47
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48 if __name__ == "__main__":
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49 main()
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