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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/taxonomy/t2ps commit a1517c9d22029095120643bbe2c8fa53754dd2b7
author | devteam |
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date | Wed, 11 Nov 2015 12:56:38 -0500 |
parents | 9e2b9ca7f33a |
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""" Wrapper for tree2PS-fast Requires ps2pdf (a part of ghostscript package) to be installed t2ps_wrapper.py <taxonomy file> <output PDF file> <max_tree_level> <font_size> <max_leaves> <count_duplicate_tax_id> taxonomy file - tree file produced by taxonomy2tree program written by Sergei Kosakovski Pond output PDF file - tree image max_tree_level - integer from 0 to 21; 0 = show all levels font_size - integer from 2 to 255 (8 is the best) max_leaves - integer from 0 to infinity (0 = show all) count_duplicate - 0 (do not count) or 1 (count) anton nekrutenko | anton@bx.psu.edu tree2PS-fast is written by Sergei Kosakovski Pond | sergeilkp@mac.com """ import string, sys, tempfile, subprocess def stop_err(msg): sys.stderr.write(msg) sys.exit() try: tree_file = sys.argv[1] pdf_file = sys.argv[2] max_tree_level = sys.argv[3] font_size = sys.argv[4] max_leaves = sys.argv[5] dups = sys.argv[6] except: stop_err('Check arguments\n') newick_file = tempfile.NamedTemporaryFile('w') ps_file = tempfile.NamedTemporaryFile('w') # Execute taxonomy2tree try: t2t_cmd = 'taxonomy2tree %s %s %s /dev/null 1 > /dev/null 2>&1' % ( tree_file, max_tree_level, newick_file.name ) retcode = subprocess.call( t2t_cmd, shell=True ) if retcode < 0: print >>sys.stderr, "Execution of taxonomy2tree terminated by signal", -retcode except OSError, e: print >>sys.stderr, "Execution of taxonomy2tree failed:", e # Execute tree2PS-fast try: t2ps_cmd = 'tree2PS-fast %s %s %s %s %s %s' % ( newick_file.name, ps_file.name, max_tree_level, font_size, max_leaves, dups ) retcode = subprocess.call( t2ps_cmd, shell=True ) if retcode < 0: print >>sys.stderr, "Execution of tree2PS-fast terminated by signal", -retcode except OSError, e: print >>sys.stderr, "Execution of tree2PS-fast failed:", e # Convert PS to PDF try: ps2pdf_cmd = 'ps2pdf %s %s' % ( ps_file.name, pdf_file ) retcode = subprocess.call( ps2pdf_cmd, shell=True ) if retcode < 0: print >>sys.stderr, "Execution of ps2pdf terminated by signal", -retcode except OSError, e: print >>sys.stderr, "Execution of ps2pdf failed:", e