/tools/taxonomy/t2ps_wrapper.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 67 lines · 36 code · 12 blank · 19 comment · 10 complexity · 85b98a59c3097d4255e86f8b8b90ba37 MD5 · raw file
- """
- 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