--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/proteinpilot_wrapper.py	Wed Dec 19 00:22:55 2012 -0500
@@ -0,0 +1,326 @@
+#!/usr/bin/env python
+import optparse
+import os
+import sys
+import tempfile
+import shutil 
+import subprocess
+import re
+import time
+from os.path import basename
+import logging
+
+assert sys.version_info[:2] >= ( 2, 6 )
+
+log = logging.getLogger(__name__)
+
+DEBUG = True
+
+working_directory = os.getcwd()
+tmp_stderr_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stderr').name
+tmp_stdout_name = tempfile.NamedTemporaryFile(dir = working_directory, suffix = '.stdout').name
+
+def stop_err( msg ):
+    sys.stderr.write( "%s\n" % msg )
+    sys.exit()
+
+
+def read_stderr():
+    stderr = ''
+    if(os.path.exists(tmp_stderr_name)):
+        with open(tmp_stderr_name, 'rb') as tmp_stderr:
+            buffsize = 1048576
+            try:
+                while True:
+                    stderr += tmp_stderr.read(buffsize)
+                    if not stderr or len(stderr) % buffsize != 0:
+                        break
+            except OverflowError:
+                pass
+    return stderr
+
+
+def execute(command, stdin=None):
+    try:
+        with open(tmp_stderr_name, 'wb') as tmp_stderr:
+            with open(tmp_stdout_name, 'wb') as tmp_stdout:
+                proc = subprocess.Popen(args=command, shell=True, stderr=tmp_stderr.fileno(), stdout=tmp_stdout.fileno(), stdin=stdin, env=os.environ)
+                returncode = proc.wait()
+                if returncode != 0:
+                    raise Exception("Program returned with non-zero exit code %d. stderr: %s" % (returncode, read_stderr()))
+    finally:
+        print open(tmp_stderr_name, "r").read(64000)
+        print open(tmp_stdout_name, "r").read(64000)
+
+
+def delete_file(path):
+    if os.path.exists(path):
+        try:
+            os.remove(path)
+        except:
+            pass
+
+def delete_directory(directory):
+    if os.path.exists(directory):
+        try:
+            shutil.rmtree(directory)
+        except:
+            pass
+
+def symlink(source, link_name):
+    import platform
+    if platform.system() == 'Windows':
+        try:
+            import win32file
+            win32file.CreateSymbolicLink(source, link_name, 1)
+        except:
+            shutil.copy(source, link_name)
+    else:
+        os.symlink(source, link_name)
+
+
+def copy_to_working_directory(data_file, relative_path):
+    if os.path.abspath(data_file) != os.path.abspath(relative_path):
+        shutil.copy(data_file, relative_path)
+    return relative_path
+
+def __main__():
+    run_script()
+
+#ENDTEMPLATE
+
+from string import Template
+
+METHOD_TEMPLATE = """<UISETTINGS>
+<UI_SAMPLE_TYPE>$sample_type</UI_SAMPLE_TYPE>
+<UI_QUANT_TYPE>$quant_type</UI_QUANT_TYPE>
+<UI_BACKGROUND_CORRECTION>$background_correction</UI_BACKGROUND_CORRECTION>
+<UI_BIAS_CORRECTION>$bias_correction</UI_BIAS_CORRECTION>
+<UI_CYS_ALKYLATION>$cys_alkylation</UI_CYS_ALKYLATION>
+<UI_DIGESTION>$digestion</UI_DIGESTION>
+<UI_SPECIAL_FACTOR>$special_factors</UI_SPECIAL_FACTOR>
+<UI_INSTRUMENT>$instrument</UI_INSTRUMENT>
+<UI_SPECIES></UI_SPECIES>
+<UI_USER_NAME></UI_USER_NAME>
+<UI_MACHINE_NAME></UI_MACHINE_NAME>
+<UI_START_TIME></UI_START_TIME>
+<UI_SEARCH_ID></UI_SEARCH_ID>
+<UI_ID_FOCUS>$search_foci</UI_ID_FOCUS>
+<UI_SEARCH_EFFORT>$search_effort</UI_SEARCH_EFFORT>
+<UI_SEARCH_RESOURCE>$database_name</UI_SEARCH_RESOURCE>
+<UI_MIN_UNUSED_PROTSCORE>$min_unused_protscore</UI_MIN_UNUSED_PROTSCORE>
+<UI_PSPEP>$pspep</UI_PSPEP>
+<UI_MAX_QUANT_LABELS>$max_quant_labels</UI_MAX_QUANT_LABELS>
+$quant_labels
+</UISETTINGS>
+"""
+
+quant_special_cases = {
+    "iTRAQ 4plex (Peptide Labeled)": "iTRAQ4PLEX",
+    "iTRAQ 4plex (Protein Labeled)": "iTRAQ4PLEX",
+    "iTRAQ 8plex (Peptide Labeled)": "iTRAQ8PLEX",
+    "iTRAQ 8plex (Protein Labeled)": "iTRAQ8PLEX",
+    "mTRAQ (Peptide Labeled - M00, M04)": "mTRAQ_0-4",
+    "mTRAQ (Peptide Labeled - M00, M08)": "mTRAQ_0-8",
+    "mTRAQ (Peptide Labeled - M04, M08)": "mTRAQ_4-8",
+    "mTRAQ (Peptide Labeled - M00, M04, M08)": "mTRAQ_0-4-8",
+    "Proteolytic O-18 labeling": "Proteolytic O-18 v O-16",
+    "Cleavable ICAT": "ICAT9",
+    "ICPL Light, Heavy (Peptide Labeled)": "ICPL peptide",
+    "ICPL Light, Heavy (Protein Labeled)": "ICPL protein",
+}
+
+
+def get_env_property(name, default):
+    if name in os.environ:
+        return os.environ[name]
+    else:
+        return default
+
+
+def build_quant_label(reagent, quant_type="Not Used", treatment="", minus2="0", minus1="0", plus1="0", plus2="0"):
+    return {
+    "reagent": reagent,
+    "type": quant_type,
+    "treatment": treatment,
+    "minus2": minus2,
+    "minus1": minus1,
+    "plus1": plus1,
+    "plus2": plus2,
+    }
+
+
+def build_quant_labels(options, quant_type):
+    if quant_type == "iTRAQ8PLEX":
+        return [
+            build_quant_label("iTRAQ113", plus1="6.89", plus2="0.24"),
+            build_quant_label("iTRAQ114", minus1="0.94", plus1="5.9", plus2="0.16"),
+            build_quant_label("iTRAQ115", minus1="1.88", plus1="4.9", plus2="0.1"),
+            build_quant_label("iTRAQ116", minus1="2.82", plus1="3.9", plus2="0.07"),
+            build_quant_label("iTRAQ117", minus2="0.06", minus1="3.77", plus1="2.88"),
+            build_quant_label("iTRAQ118", minus2="0.09", minus1="4.71", plus1="1.91"),
+            build_quant_label("iTRAQ119", minus2="0.14", minus1="5.66", plus1="0.87"),
+            build_quant_label("iTRAQ121", minus2="0.27", minus1="7.44", plus1="0.18"),
+        ]
+    elif quant_type == "iTRAQ4PLEX":
+        return [
+            build_quant_label("iTRAQ114", minus1="1.00", plus1="5.9", plus2="0.20"),
+            build_quant_label("iTRAQ115", minus1="2.00", plus1="5.6", plus2="0.1"),
+            build_quant_label("iTRAQ116", minus1="3.00", plus1="4.5", plus2="0.1"),
+            build_quant_label("iTRAQ117", minus2="0.10", minus1="4.00", plus1="3.50", plus2="0.1"),
+        ]
+    else:
+        return []
+
+
+def join_quant_labels(labels):
+    template = '<QUANT_LABEL_SETTING reagent="$reagent" type="$type" treatment="$treatment" minus2="$minus2" minus1="$minus1" plus1="$plus1" plus2="$plus2"/>'
+    return "\n".join([Template(template).substitute(quant_label) for quant_label in labels])
+
+
+def handle_sample_type(options, parameter_dict):
+    sample_type = options.sample_type
+    if sample_type in quant_special_cases:
+        quant_type = quant_special_cases[sample_type]
+    else:
+        quant_type = sample_type
+    if options.quantitative.upper() != "TRUE":
+        quant_type = ""
+    parameter_dict["sample_type"] = sample_type
+    parameter_dict["quant_type"] = quant_type
+    parameter_dict["quant_labels"] = join_quant_labels(build_quant_labels(options, quant_type))
+
+
+def setup_database(options):
+    PROTEINPILOT_DATABASE_DIR = get_env_property("PROTEIN_PILOT_DATABASE_FOLDER", "C:\\AB SCIEX\\ProteinPilot Data\\SearchDatabases")
+    database_path = options.database
+    database_name = options.database_name
+    database_name = database_name.replace(" ", "_")
+    (database_basename, extension) = os.path.splitext(database_name)
+    base = os.path.join(PROTEINPILOT_DATABASE_DIR, "gx_%s" % database_basename)
+    database_destination = get_unique_path(base, ".fasta")
+    symlink(database_path, database_destination)
+    return (database_destination, os.path.basename(os.path.splitext(database_destination)[0]))
+
+
+def extract_list(parameter):
+    if parameter == None or parameter == "None":
+        parameter = ""
+    return parameter.replace(",", ";")
+
+
+def setup_methods(options):
+    ## Setup methods file
+    (database_path, database_name) = setup_database(options)
+    special_factors = extract_list(options.special_factors)
+    search_foci = extract_list(options.search_foci)
+    method_parameters = {
+        "background_correction": options.background_correction,
+        "bias_correction": options.bias_correction,
+        "cys_alkylation": options.cys_alkylation,
+        "digestion": options.digestion,
+        "instrument": options.instrument,
+        "search_effort": options.search_effort,
+        "search_foci": search_foci,
+        "pspep": options.pspep,
+        "min_unused_protscore": options.min_unused_protscore,
+        "max_quant_labels": "3",
+        "database_name": database_name,
+        "quantitative": options.quantitative,
+        "special_factors": special_factors
+    }
+    handle_sample_type(options, method_parameters)
+    method_contents = Template(METHOD_TEMPLATE).substitute(method_parameters)
+    PROTEINPILOT_METHODS_DIR = get_env_property("PROTEIN_PILOT_METHODS_FOLDER", "C:\\ProgramData\\AB SCIEX\\ProteinPilot\\ParagonMethods\\")
+    methods_name = "gx_%s" % os.path.split(os.getcwd())[-1]
+    methods_path = os.path.join(PROTEINPILOT_METHODS_DIR, "%s.xml" % methods_name)
+    open(methods_path, "w").write(method_contents)
+    return (methods_name, methods_path, database_path)
+
+
+def setup_inputs(inputs, input_names):
+    links = []
+    for input, input_name in zip(inputs, input_names):
+        if DEBUG:
+            print "Processing input %s with name %s and size %d" % (input, input_name, os.stat(input).st_size)
+        if not input_name.upper().endswith(".MGF"):
+            input_name = "%s.mgf" % input_name
+        link_path = os.path.abspath(input_name)
+        symlink(input, link_path)
+        links.append(link_path)
+    return ",".join(["<DATA type=\"MGF\" filename=\"%s\" />" % link for link in links])
+
+
+def get_unique_path(base, extension):
+    """
+    """
+    return "%s_%d%s" % (base, int(time.time() * 1000), extension)
+
+
+def move_pspep_output(options, destination, suffix):
+    if destination:
+        source = "%s__FalsePositiveAnalysis__%s.csv" % (options.output, suffix)
+        shutil.move(source, destination)
+
+
+def run_script():
+    parser = optparse.OptionParser()
+    parser.add_option("--input", dest="input", action="append", default=[])
+    parser.add_option("--input_name", dest="input_name", action="append", default=[])
+    parser.add_option("--database")
+    parser.add_option("--database_name")
+    parser.add_option("--instrument")
+    parser.add_option("--sample_type")  # TODO: Restrict values
+    parser.add_option("--bias_correction", default="False")
+    parser.add_option("--background_correction", default="False")
+    parser.add_option("--cys_alkylation", default="None")
+    parser.add_option("--digestion", default="Trypsin")
+    parser.add_option("--special_factors", default="")
+    parser.add_option("--search_foci", default="")
+    parser.add_option("--search_effort", default="Rapid")
+    parser.add_option("--min_unused_protscore", default="3")
+    parser.add_option("--quantitative", default="False")
+    parser.add_option("--pspep", default="TRUE")
+    parser.add_option("--output")
+    parser.add_option("--output_methods")
+    #parser.add_option("--output_pspep_peptide", default="")
+    #parser.add_option("--output_pspep_protein", default="")
+    #parser.add_option("--output_pspep_spectra", default="")
+    parser.add_option("--output_pspep_report", default="")
+    (options, args) = parser.parse_args()
+
+    (methods_name, methods_path, database_path) = setup_methods(options)
+    try:
+        group_file = "%s.group" % options.output
+        input_contents_template = """<PROTEINPILOTPARAMETERS>
+    <METHOD name="$methods_name" />
+    $inputs
+    <RESULT filename="$output" />
+</PROTEINPILOTPARAMETERS>"""
+        input_parameters = {
+            "inputs": setup_inputs(options.input, options.input_name),
+            "output": group_file,
+            "methods_name": methods_name
+        }
+
+        input_contents = Template(input_contents_template).substitute(input_parameters)
+        open("input.xml", "w").write(input_contents)
+
+        protein_pilot_path = get_env_property("PROTEIN_PILOT_PATH", "")
+        if protein_pilot_path and not protein_pilot_path.endswith("\\"):
+            protein_pilot_path = "%s" % protein_pilot_path
+        execute("%sProteinPilot.exe input.xml" % protein_pilot_path)
+        shutil.move(group_file, options.output)
+        #move_pspep_output(options, options.output_pspep_spectra, "SpectralLevelData")
+        #move_pspep_output(options, options.output_pspep_peptide, "DistinctPeptideLevelData")
+        #move_pspep_output(options, options.output_pspep_protein, "ProteinLevelData")
+        if options.output_pspep_report:
+            source = "%s__FDR.xlsx" % (options.output)
+            shutil.move(source, options.output_pspep_report)
+        shutil.move(methods_path, options.output_methods)
+    finally:
+        delete_file(database_path)
+        delete_file(methods_path)
+
+if __name__ == '__main__':
+    __main__()