comparison ffp_phylogeny.py @ 1:d1c88b118a3f draft

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0:eb6e5e78a066

#!/usr/bin/python
import optparse
import time
import os
import tempfile
import sys
import shlex, subprocess

	"""
	commands = command.split("|")
	processes = []
	ptr = 0
	for command_line in commands:
		print command_line.strip()
		args = shlex.split(command_line.strip())
		if ptr == 0:
			proc = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
			processes.append(proc)
		else:
			# 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.
			stderrdata = processes[ptr-1].stderr.read()
			retcode = processes[ptr-1].poll()
			if retcode or len(stderrdata) > 0:
				stop_err(stderrdata)

			newProcess = subprocess.Popen(args, stdin=processes[ptr-1].stdout, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
			processes.append(newProcess)
			processes[ptr-1].stdout.close() # Allow prev. process to receive a SIGPIPE if current process exits.
		
		ptr += 1

	(stdoutdata, stderrdata) = processes[ptr-1].communicate()
	retcode = processes[ptr-1].poll()
	if retcode or len(stderrdata) > 0:
		stop_err(stderrdata)
	
	return stdoutdata
	

		command += ' | ffprwn'

		#Now create a taxonomy label file, ensuring a name exists for each profile.
		taxonomyNames = getTaxonomyNames(options.type, options.multiple, options.abbreviate, in_files, options.taxonomy)
		taxonomyTempFile = getTaxonomyFile(taxonomyNames)
		# -p = Include phylip format 'infile' of the taxon names to use.  Very simple, just a list of fasta identifier names.
		command += ' | ffpjsd -p ' + taxonomyTempFile

		if options.metric and len(options.metric) >0 :
			command += ' --' + options.metric

			if len(taxonomyNames) > 2:
				command += ' | ffptree -q' 
			else:
				stop_err("For a phylogenetic tree display, one must have at least 3 ffp profiles.")

		result = check_output(command)
		with open(options.output,'w') as fw:
			fw.writelines(result)
		os.remove(taxonomyTempFile)

1:d1c88b118a3f

#!/usr/bin/python
import optparse
import re
import time
import os
import tempfile
import sys
import shlex, subprocess

	"""
	commands = command.split("|")
	processes = []
	ptr = 0
	substantive = re.compile('[a-zA-Z0-9]+')
	
	for command_line in commands:
		print command_line.strip()
		args = shlex.split(command_line.strip())
		if ptr == 0:
			proc = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
			processes.append(proc)
		else:

			#this has to come before error processing?
			newProcess = subprocess.Popen(args, stdin=processes[ptr-1].stdout, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
			
			# 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.
		
		ptr += 1

	retcode = processes[ptr-1].poll()
	(stdoutdata, stderrdata) = processes[ptr-1].communicate()
	if retcode or (len(stderrdata) > 0 and substantive.search(stderrdata)):
		stop_err(stderrdata)
	
	return stdoutdata
	

		command += ' | ffprwn'

		#Now create a taxonomy label file, ensuring a name exists for each profile.
		taxonomyNames = getTaxonomyNames(options.type, options.multiple, options.abbreviate, in_files, options.taxonomy)
		taxonomyTempFile = getTaxonomyFile(taxonomyNames)
		
		# -p = Include phylip format 'infile' of the taxon names to use.  Very simple, just a list of fasta identifier names.
		command += ' | ffpjsd -p ' + taxonomyTempFile

		if options.metric and len(options.metric) >0 :
			command += ' --' + options.metric

			if len(taxonomyNames) > 2:
				command += ' | ffptree -q' 
			else:
				stop_err("For a phylogenetic tree display, one must have at least 3 ffp profiles.")

		#print command
		
		result = check_output(command)
		with open(options.output,'w') as fw:
			fw.writelines(result)
		os.remove(taxonomyTempFile)