comparison tools/effectiveT3/effectiveT3.py @ 5:1ea715da1879 draft

Uploaded v0.0.13, embed citation, relax test for floating point differences

4:f7ce32e13bc6

"""
import sys
import os
import subprocess

#The Galaxy auto-install via tool_dependencies.xml will set this environment variable
effectiveT3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
effectiveT3_jar = os.path.join(effectiveT3_dir, "TTSS_GUI-1.0.1.jar")

if "-v" in sys.argv or "--version" in sys.argv:
    #TODO - Get version of the JAR file dynamically?
    print "Wrapper v0.0.11, TTSS_GUI-1.0.1.jar"
    sys.exit(0)

def stop_err(msg, error_level=1):
   """Print error message to stdout and quit with given error level."""
   sys.stderr.write("%s\n" % msg)

    for line in raw_handle:
        if not line or line.startswith("#") \
        or line.startswith("Id; Description; Score;"):
            continue
        assert line.count(";") >= 3, repr(line)
        #Normally there will just be three semi-colons, however the
        #original FASTA file's ID or description might have had
        #semi-colons in it as well, hence the following hackery:
        try:
            id_descr, score, effective = line.rstrip("\r\n").rsplit(";",2)
            #Cope when there was no FASTA description
            if "; " not in id_descr and id_descr.endswith(";"):
                id = id_descr[:-1]
                descr = ""
            else:
                id, descr = id_descr.split("; ",1)

        if effective.lower() == "true":
           positive += 1
    return count, positive, errors

def run(cmd):
    #Avoid using shell=True when we call subprocess to ensure if the Python
    #script is killed, so too is the child process.
    try:
        child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    except Exception, err:
        stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
    #Use .communicate as can get deadlocks with .wait(),
    stdout, stderr = child.communicate()
    return_code = child.returncode
    if return_code:
        if stderr and stdout:
            stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, err, stdout, stderr))
        else:
            stop_err("Return code %i from command:\n%s\n%s" % (return_code, err, stderr))

if not os.path.isdir(effectiveT3_dir):
    stop_err("Effective T3 folder not found: %r" % effectiveT3_dir)

if not os.path.isfile(effectiveT3_jar):

                     % (os.path.join(effectiveT3_dir, "module"),
                        ", ".join(repr(p) for p in os.listdir(os.path.join(effectiveT3_dir, "module")))))
    sys.stderr.write("Main JAR was found: %r\n" % effectiveT3_jar)
    stop_err("Effective T3 model JAR file not found: %r" % effectiveT3_model)

#We will have write access whereever the output should be,
temp_file = os.path.abspath(tabular_file + ".tmp")

#Use absolute paths since will change current directory...
tabular_file = os.path.abspath(tabular_file)
fasta_file = os.path.abspath(fasta_file)

cmd = ["java", "-jar", effectiveT3_jar,
       "-f", fasta_file,

       "-t", threshold,
       "-o", temp_file,
       "-q"]

try:
    #Must run from directory above the module subfolder:
    os.chdir(effectiveT3_dir)
except:
    stop_err("Could not change to Effective T3 folder: %s" % effectiveT3_dir)

run(cmd)

out_handle.close()

os.remove(temp_file)

if errors:
   print "%i sequences, %i positive, %i errors" \
         % (count, positive, errors)
else:
   print "%i/%i sequences positive" % (positive, count)

if count and count==errors:
   #Galaxy will still  allow them to see the output file
   stop_err("All your sequences gave an error code")

5:1ea715da1879

"""
import sys
import os
import subprocess

# The Galaxy auto-install via tool_dependencies.xml will set this environment variable
effectiveT3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
effectiveT3_jar = os.path.join(effectiveT3_dir, "TTSS_GUI-1.0.1.jar")

if "-v" in sys.argv or "--version" in sys.argv:
    # TODO - Get version of the JAR file dynamically?
    print("Wrapper v0.0.13, TTSS_GUI-1.0.1.jar")
    sys.exit(0)

def stop_err(msg, error_level=1):
   """Print error message to stdout and quit with given error level."""
   sys.stderr.write("%s\n" % msg)

    for line in raw_handle:
        if not line or line.startswith("#") \
        or line.startswith("Id; Description; Score;"):
            continue
        assert line.count(";") >= 3, repr(line)
        # Normally there will just be three semi-colons, however the
        # original FASTA file's ID or description might have had
        # semi-colons in it as well, hence the following hackery:
        try:
            id_descr, score, effective = line.rstrip("\r\n").rsplit(";",2)
            # Cope when there was no FASTA description
            if "; " not in id_descr and id_descr.endswith(";"):
                id = id_descr[:-1]
                descr = ""
            else:
                id, descr = id_descr.split("; ",1)

        if effective.lower() == "true":
           positive += 1
    return count, positive, errors

def run(cmd):
    # Avoid using shell=True when we call subprocess to ensure if the Python
    # script is killed, so too is the child process.
    try:
        child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    except Exception, err:
        stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
    # Use .communicate as can get deadlocks with .wait(),
    stdout, stderr = child.communicate()
    return_code = child.returncode
    if return_code:
        cmd_str= " ".join(cmd)  # doesn't quote spaces etc
        if stderr and stdout:
            stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
        else:
            stop_err("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))

if not os.path.isdir(effectiveT3_dir):
    stop_err("Effective T3 folder not found: %r" % effectiveT3_dir)

if not os.path.isfile(effectiveT3_jar):

                     % (os.path.join(effectiveT3_dir, "module"),
                        ", ".join(repr(p) for p in os.listdir(os.path.join(effectiveT3_dir, "module")))))
    sys.stderr.write("Main JAR was found: %r\n" % effectiveT3_jar)
    stop_err("Effective T3 model JAR file not found: %r" % effectiveT3_model)

# We will have write access whereever the output should be,
temp_file = os.path.abspath(tabular_file + ".tmp")

# Use absolute paths since will change current directory...
tabular_file = os.path.abspath(tabular_file)
fasta_file = os.path.abspath(fasta_file)

cmd = ["java", "-jar", effectiveT3_jar,
       "-f", fasta_file,

       "-t", threshold,
       "-o", temp_file,
       "-q"]

try:
    # Must run from directory above the module subfolder:
    os.chdir(effectiveT3_dir)
except:
    stop_err("Could not change to Effective T3 folder: %s" % effectiveT3_dir)

run(cmd)

out_handle.close()

os.remove(temp_file)

if errors:
   print("%i sequences, %i positive, %i errors"
         % (count, positive, errors))
else:
   print("%i/%i sequences positive" % (positive, count))

if count and count==errors:
   # Galaxy will still  allow them to see the output file
   stop_err("All your sequences gave an error code")