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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