comparison ffp_phylogeny.py @ 2:671667722d3d draft

fix: ffptree taxonomy name file convert () to _

1:d1c88b118a3f

import tempfile
import sys
import shlex, subprocess
from string import maketrans

VERSION_NUMBER = "0.1.00"

class MyParser(optparse.OptionParser):
	"""
	 From http://stackoverflow.com/questions/1857346/python-optparse-how-to-include-additional-info-in-usage-output
	 Provides a better class for displaying formatted help info in epilog() portion of optParse; allows for carriage returns.

	@filepaths array resulting galaxy dataset file .dat paths
	
	"""
	# Take off prefix/suffix whitespace/comma :
	taxonomy = filenames.strip().strip(',').split(',')
	translations = maketrans(' .-	','____')
	names=[]
	ptr = 0

	for file in filepaths:
		# First, convert space, period to underscore in file names.	  ffprwn IS VERY SENSITIVE ABOUT THIS.
		# Also trim labels to 50 characters.  Turns out ffpjsd is kneecapping a taxonomy label to 10 characters if it is greater than 50 chars.
		taxonomyitem = taxonomy[ptr].strip().translate(translations)[:50]
		# print taxonomyitem
		if not type in 'text' and multiple:
			#Must read each fasta file, looking for all lines beginning ">"
			with open(file) as fastafile:
				lineptr = 0
				for line in fastafile:
					if line[0] == '>':

						# Odd case where no fasta description found
						if name == '': name = taxonomyitem + '.' + str(lineptr)
						names.append(name)
						lineptr += 1
		else:
			names.append(taxonomyitem)
		
		ptr += 1

	if abbreviate:

			
			# It seems the act of reading standard error output is enough to trigger
			# error code signal for that process, i.e. so that retcode returns a code.
			retcode = processes[ptr-1].poll()
			stderrdata = processes[ptr-1].stderr.read()
			#Issue with ffptree is it outputs ----....---- on stderr
			if retcode or (len(stderrdata) > 0 and substantive.search(stderrdata)):
				stop_err(stderrdata)			

			processes.append(newProcess)			
			processes[ptr-1].stdout.close() # Allow prev. process to receive a SIGPIPE if current process exits.

2:671667722d3d

import tempfile
import sys
import shlex, subprocess
from string import maketrans

VERSION_NUMBER = "0.1.03"

class MyParser(optparse.OptionParser):
	"""
	 From http://stackoverflow.com/questions/1857346/python-optparse-how-to-include-additional-info-in-usage-output
	 Provides a better class for displaying formatted help info in epilog() portion of optParse; allows for carriage returns.

	@filepaths array resulting galaxy dataset file .dat paths
	
	"""
	# Take off prefix/suffix whitespace/comma :
	taxonomy = filenames.strip().strip(',').split(',')
	names=[]
	ptr = 0

	for file in filepaths:
		# Trim labels to 50 characters max.  ffpjsd kneecaps a taxonomy label to 10 characters if it is greater than 50 chars.
		taxonomyitem = taxonomy[ptr].strip()[:50] #.translate(translations)
		# Convert non-alphanumeric characters to underscore in taxonomy names.  ffprwn IS VERY SENSITIVE ABOUT THIS.
		taxonomyitem = re.sub('[^0-9a-zA-Z]+', '_', taxonomyitem)

		if (not type in 'text') and multiple:
			#Must read each fasta file, looking for all lines beginning ">"
			with open(file) as fastafile:
				lineptr = 0
				for line in fastafile:
					if line[0] == '>':

						# Odd case where no fasta description found
						if name == '': name = taxonomyitem + '.' + str(lineptr)
						names.append(name)
						lineptr += 1
		else:

			names.append(taxonomyitem)
		
		ptr += 1

	if abbreviate:

			
			# It seems the act of reading standard error output is enough to trigger
			# error code signal for that process, i.e. so that retcode returns a code.
			retcode = processes[ptr-1].poll()
			stderrdata = processes[ptr-1].stderr.read()
			#Issue with ffptree is it outputs ---- ... ---- on stderr even when ok.
			if retcode or (len(stderrdata) > 0 and substantive.search(stderrdata)):
				stop_err(stderrdata)			

			processes.append(newProcess)			
			processes[ptr-1].stdout.close() # Allow prev. process to receive a SIGPIPE if current process exits.