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1 """
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2 Wrapper for tree2PS-fast
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3 Requires ps2pdf (a part of ghostscript package) to be installed
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4
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5 t2ps_wrapper.py <taxonomy file> <output PDF file> <max_tree_level> <font_size> <max_leaves> <count_duplicate_tax_id>
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6
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7 taxonomy file - tree file produced by taxonomy2tree program written by Sergei Kosakovski Pond
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8 output PDF file - tree image
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9 max_tree_level - integer from 0 to 21; 0 = show all levels
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10 font_size - integer from 2 to 255 (8 is the best)
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11 max_leaves - integer from 0 to infinity (0 = show all)
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12 count_duplicate - 0 (do not count) or 1 (count)
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13
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14 anton nekrutenko | anton@bx.psu.edu
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15 tree2PS-fast is written by Sergei Kosakovski Pond | sergeilkp@mac.com
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16 """
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17
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18 import string, sys, tempfile, subprocess
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19
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20 def stop_err(msg):
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21 sys.stderr.write(msg)
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22 sys.exit()
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23
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24
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25 try:
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26 tree_file = sys.argv[1]
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27 pdf_file = sys.argv[2]
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28 max_tree_level = sys.argv[3]
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29 font_size = sys.argv[4]
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30 max_leaves = sys.argv[5]
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31 dups = sys.argv[6]
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32 except:
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33 stop_err('Check arguments\n')
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34
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35 newick_file = tempfile.NamedTemporaryFile('w')
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36 ps_file = tempfile.NamedTemporaryFile('w')
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37
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38 # Execute taxonomy2tree
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39
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40 try:
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41 t2t_cmd = 'taxonomy2tree %s %s %s /dev/null 1 > /dev/null 2>&1' % ( tree_file, max_tree_level, newick_file.name )
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42 retcode = subprocess.call( t2t_cmd, shell=True )
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43 if retcode < 0:
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44 print >>sys.stderr, "Execution of taxonomy2tree terminated by signal", -retcode
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45 except OSError, e:
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46 print >>sys.stderr, "Execution of taxonomy2tree failed:", e
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47
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48
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49 # Execute tree2PS-fast
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50
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51 try:
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52 t2ps_cmd = 'tree2PS-fast %s %s %s %s %s %s' % ( newick_file.name, ps_file.name, max_tree_level, font_size, max_leaves, dups )
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53 retcode = subprocess.call( t2ps_cmd, shell=True )
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54 if retcode < 0:
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55 print >>sys.stderr, "Execution of tree2PS-fast terminated by signal", -retcode
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56 except OSError, e:
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57 print >>sys.stderr, "Execution of tree2PS-fast failed:", e
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58
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59 # Convert PS to PDF
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60
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61 try:
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62 ps2pdf_cmd = 'ps2pdf %s %s' % ( ps_file.name, pdf_file )
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63 retcode = subprocess.call( ps2pdf_cmd, shell=True )
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64 if retcode < 0:
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65 print >>sys.stderr, "Execution of ps2pdf terminated by signal", -retcode
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66 except OSError, e:
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67 print >>sys.stderr, "Execution of ps2pdf failed:", e
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