comparison tools/effectiveT3/effectiveT3.py @ 32:1129cafdf0ae draft

planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty

31:3ef6c246ccac

It then calls the standalone Effective T3 v1.0.1 program (not the
webservice), and reformats the semi-colon separated output into
tab separated output for use in Galaxy.
"""
import os
import subprocess
import sys

# The Galaxy auto-install via tool_dependencies.xml will set this environment variable
effective_t3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
effective_t3_jar = os.path.join(effective_t3_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 v0.0.19, TTSS_GUI-1.0.1.jar")
    sys.exit(0)

if len(sys.argv) != 5:
    sys.exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file")

            sys.exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
        else:
            sys.exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))


if not os.path.isdir(effective_t3_dir):
    sys.exit("Effective T3 folder not found: %r" % effective_t3_dir)

if not os.path.isfile(effective_t3_jar):
    sys.exit("Effective T3 JAR file not found: %r" % effective_t3_jar)

if not os.path.isdir(os.path.join(effective_t3_dir, "module")):
    sys.exit("Effective T3 module folder not found: %r" % os.path.join(effective_t3_dir, "module"))

effective_t3_model = os.path.join(effective_t3_dir, "module", model)

                        ", ".join(repr(p) for p in os.listdir(os.path.join(effective_t3_dir, "module")))))
    sys.stderr.write("Main JAR was found: %r\n" % effective_t3_jar)
    sys.exit("Effective T3 model JAR file not found: %r" % effective_t3_model)

# We will have write access wherever 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)

32:1129cafdf0ae

It then calls the standalone Effective T3 v1.0.1 program (not the
webservice), and reformats the semi-colon separated output into
tab separated output for use in Galaxy.
"""
import os
# We want to be able to use shutil.which, but need Python 3.3+
# import shutil
import subprocess
import sys

# The Galaxy auto-install via tool_dependencies.xml will set the
# environment variable $EFFECTIVET3 pointing at the folder with
# the JAR file.
#
# The BioConda recipe will put a wrapper script on the $PATH,
# which we can use to find the JAR file.
#
# We fall back on /opt/EffectiveT3/
#
effective_t3_jarname = "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 v0.0.20, for %s" % effective_t3_jarname)
    sys.exit(0)

if len(sys.argv) != 5:
    sys.exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file")

            sys.exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
        else:
            sys.exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))


try:
    from shutil import which
except ImportError:
    # Likely running on Python 2, use backport:
    def which(cmd, mode=os.F_OK | os.X_OK, path=None):
        """Given a command, mode, and a PATH string, return the path which
        conforms to the given mode on the PATH, or None if there is no such
        file.
        `mode` defaults to os.F_OK | os.X_OK. `path` defaults to the result
        of os.environ.get("PATH"), or can be overridden with a custom search
        path.
        """

        # Check that a given file can be accessed with the correct mode.
        # Additionally check that `file` is not a directory, as on Windows
        # directories pass the os.access check.
        def _access_check(fn, mode):
            return (os.path.exists(fn) and os.access(fn, mode) and
                    not os.path.isdir(fn))

        # Short circuit. If we're given a full path which matches the mode
        # and it exists, we're done here.
        if _access_check(cmd, mode):
            return cmd

        path = (path or os.environ.get("PATH", os.defpath)).split(os.pathsep)

        if sys.platform == "win32":
            # The current directory takes precedence on Windows.
            if os.curdir not in path:
                path.insert(0, os.curdir)

            # PATHEXT is necessary to check on Windows.
            pathext = os.environ.get("PATHEXT", "").split(os.pathsep)
            # See if the given file matches any of the expected path extensions.
            # This will allow us to short circuit when given "python.exe".
            matches = [cmd for ext in pathext if cmd.lower().endswith(ext.lower())]
            # If it does match, only test that one, otherwise we have to try
            # others.
            files = [cmd] if matches else [cmd + ext.lower() for ext in pathext]
        else:
            # On other platforms you don't have things like PATHEXT to tell you
            # what file suffixes are executable, so just pass on cmd as-is.
            files = [cmd]

        seen = set()
        for dir in path:
            dir = os.path.normcase(dir)
            if dir not in seen:
                seen.add(dir)
                for thefile in files:
                    name = os.path.join(dir, thefile)
                    if _access_check(name, mode):
                        return name
        return None


# Try in order the following to find the JAR file:
# - Location of any wrapper script, e.g. from BioConda installation
# - The $EFFECTIVET3 env var, e.g. old-style Galaxy tool installation
# - The /opt/EffectiveT3/ folder.
effective_t3_jar = None
effective_t3_dir = None
dirs = ["/opt/EffectiveT3/"]
if "EFFECTIVET3" in os.environ:
    dirs.insert(0, os.environ.get("EFFECTIVET3"))
if which("effectivet3"):
    # Assuming this is a BioConda installed wrapper for effective T3,
    # this will get the directory of the wrapper script which is where
    # the JAR file will be:
    dirs.insert(0, os.path.split(os.path.realpath(which("effectivet3")))[0])
for effective_t3_dir in dirs:
    effective_t3_jar = os.path.join(effective_t3_dir, effective_t3_jarname)
    if os.path.isfile(effective_t3_jar):
        # Good
        break
    effective_t3_jar = None
if not effective_t3_dir or not effective_t3_jar:
    sys.exit("Effective T3 JAR file %r not found in %r" % (effective_t3_jarname, dirs))

if not os.path.isdir(os.path.join(effective_t3_dir, "module")):
    sys.exit("Effective T3 module folder not found: %r" % os.path.join(effective_t3_dir, "module"))

effective_t3_model = os.path.join(effective_t3_dir, "module", model)

                        ", ".join(repr(p) for p in os.listdir(os.path.join(effective_t3_dir, "module")))))
    sys.stderr.write("Main JAR was found: %r\n" % effective_t3_jar)
    sys.exit("Effective T3 model JAR file not found: %r" % effective_t3_model)

# We will have write access wherever the output should be,
if tabular_file == "/dev/stdout":
    temp_file = os.path.abspath("effectivet3_tabular_output.tmp")
else:
    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)