comparison tools/effectiveT3/effectiveT3.py @ 35:e2711662802b draft default tip

planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit d67596914a7bbe183851437eaafe8c7305877e5a-dirty

34:011cfce866f1

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

    # 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")

model, threshold, fasta_file, tabular_file = sys.argv[1:]

if not os.path.isfile(fasta_file):
    sys.exit("Input FASTA file not found: %s" % fasta_file)

if threshold not in ["selective", "sensitive"] and not threshold.startswith("cutoff="):
    sys.exit("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold)


def clean_tabular(raw_handle, out_handle):
    """Clean up Effective T3 output to make it tabular."""
    count = 0
    positive = 0
    errors = 0
    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:

def run(cmd):
    """Run the command line string via subprocess."""
    # 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, universal_newlines=True,
                                 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    except Exception as err:
        sys.exit("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 or stderr.startswith("Exception in thread"):
        cmd_str = " ".join(cmd)  # doesn't quote spaces etc
        if stderr and stdout:
            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:

        """
        # 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

    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)
if not os.path.isfile(effective_t3_model):
    sys.stderr.write("Contents of %r is %s\n"
                     % (os.path.join(effective_t3_dir, "module"),
                        ", ".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":

# 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", effective_t3_jar,
       "-f", fasta_file,
       "-m", model,
       "-t", threshold,
       "-o", temp_file,
       "-q"]

try:
    # Must run from directory above the module subfolder:
    os.chdir(effective_t3_dir)
except Exception:

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

35:e2711662802b

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

    # 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"
    )

model, threshold, fasta_file, tabular_file = sys.argv[1:]

if not os.path.isfile(fasta_file):
    sys.exit("Input FASTA file not found: %s" % fasta_file)

if threshold not in ["selective", "sensitive"] and not threshold.startswith("cutoff="):
    sys.exit(
        "Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold
    )


def clean_tabular(raw_handle, out_handle):
    """Clean up Effective T3 output to make it tabular."""
    count = 0
    positive = 0
    errors = 0
    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:

def run(cmd):
    """Run the command line string via subprocess."""
    # 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, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE
        )
    except Exception as err:
        sys.exit("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 or stderr.startswith("Exception in thread"):
        cmd_str = " ".join(cmd)  # doesn't quote spaces etc
        if stderr and stdout:
            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:

        """
        # 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

    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)
if not os.path.isfile(effective_t3_model):
    sys.stderr.write(
        "Contents of %r is %s\n"
        % (
            os.path.join(effective_t3_dir, "module"),
            ", ".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":

# 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",
    effective_t3_jar,
    "-f",
    fasta_file,
    "-m",
    model,
    "-t",
    threshold,
    "-o",
    temp_file,
    "-q",
]

try:
    # Must run from directory above the module subfolder:
    os.chdir(effective_t3_dir)
except Exception:

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