#!/bin/python

"""

straintables' main pipeline script;


"""

import os
import argparse
import shutil
import straintables
import subprocess

from Bio.Align.Applications import ClustalOmegaCommandline

from straintables.logo import logo

from straintables.Executable import primerFinder, detectMutations,\
    compareHeatmap, matrixAnalysis

from straintables.Database import directoryManager

Description = """

Main straintables pipeline.
Will initialize an analysis directory based on the provided genomes,
annotation and wanted regions."
If primers were not declared at the wanted regions file,
it will try to create primers based on the region sequence,
by using the region boundaries defined at the annotation file.

The resulting directory can be inspected manually
or used to build dissimilarity matrices through the command 'stview'.

"""


class Options():
    def __init__(self, options):
        self.__dict__.update(options)


def find_primers(options):

    return primerFinder.Execute(options)


def run_alignment(filePrefix,
                  clustalPath=straintables.Definitions.ClustalCommand):
    infile = filePrefix + ".fasta"
    outfile = filePrefix + ".aln"

    aln_cmd = ClustalOmegaCommandline(clustalPath,
                                      infile=infile,
                                      outfile=outfile,
                                      force=True,
                                      outfmt="clustal")
    stdout, stderr = aln_cmd()

    print(stdout)


def draw_tree(filePrefix):
    infile = filePrefix + ".ph"
    outfile = filePrefix + "pdf"

    treeOptions = Options({
        "InputFile": infile,
        "OutputFile": outfile
    })

    straintables.DrawGraphics.drawTree.Execute(treeOptions)


def run_meshclust(filePrefix):
    subprocess.run([
        "meshclust",
        filePrefix + ".fasta",
        "--output",
        filePrefix + ".clst",
        "--id", "0.999",
        "--align"
    ])


def detect_mutations(filePrefix):
    infile = filePrefix + ".aln"

    mutationsOptions = Options({
        "InputFile": infile,
        "PlotSubtitle": ""
    })

    detectMutations.Execute(mutationsOptions)


def matrix_analysis(WorkingDirectory):
    analysisOptions = Options({
        "WorkingDirectory": WorkingDirectory,
        "updateOnly": False
    })

    return matrixAnalysis.Execute(analysisOptions)


def parse_arguments():
    parser = argparse.ArgumentParser(description=Description)

    parser.add_argument("--noamplicon", dest="DoAmplicon",
                        action="store_false", default=True)

    parser.add_argument("--noalign", dest="DoAlignment",
                        action="store_false", default=True)

    parser.add_argument("--alnmode", dest="AlignmentMode",
                        default="clustal")

    parser.add_argument("--clustalpath", dest="ClustalPath",
                        default=straintables.Definitions.ClustalCommand)

    parser = primerFinder.parse_arguments(parser)

    return parser.parse_args()


def TestMeshclust():
    # -- TEST MESHCLUST SETUP;
    if shutil.which("meshclust"):
        print("MeshClust enabled!")
        return True
    else:
        print("MeshClust not found! Disabled...")
        return False


def process_individual_region(options, locusName, MeshClustEnabled):
    filePrefix = os.path.join(
        options.WorkingDirectory,
        straintables.Definitions.FastaRegionPrefix + locusName)

    print("Running alignment for %s..." % locusName)

    run_alignment(filePrefix,
                  clustalPath=options.ClustalPath)

    # draw_tree(filePrefix)
    detect_mutations(filePrefix)
    if MeshClustEnabled:
        run_meshclust(filePrefix)


def Execute(options):

    if not options.PrimerFile:
        print("Fatal: No primer file specified!")
        exit(1)

    # -- SELECT WORKING DIRECTORY;
    if not options.WorkingDirectory:
        AnalysisCode = os.path.splitext(options.PrimerFile)[0]
        AnalysisCode = os.path.basename(AnalysisCode)

        WorkingDirectoryBase = "analysisResults"
        options.WorkingDirectory = os.path.join(WorkingDirectoryBase,
                                                AnalysisCode)

    # -- TEST CLUSTAL SETUP;
    if not shutil.which(options.ClustalPath):
        print("%s not found! Aborting..." % options.ClustalPath)
        exit(1)

    MeshClustEnabled = TestMeshclust()
    directoryManager.createDirectoryPath(options.WorkingDirectory)

    # SHOW BEAUTIFUL ASCII ART;
    print(logo)

    # -- RUN PIPELINE;
    if options.DoAmplicon:
        result = find_primers(options)
        if not result:
            print("Failure to find primers.")
            exit(1)

    AllowedAlignModes = ["clustal"]
    if options.AlignmentMode not in AllowedAlignModes:
        print("Unknown alignment mode %s." % (options.AlignmentMode))
        exit(1)

    MatchedRegions = straintables.OutputFile.MatchedRegions(
        options.WorkingDirectory)
    MatchedRegions.read()

    SuccessfulLoci = MatchedRegions.content["LocusName"]

    if options.DoAlignment:
        for locusName in SuccessfulLoci:
            process_individual_region(options, locusName, MeshClustEnabled)

    if matrix_analysis(options.WorkingDirectory):
        print("Analysis successful.")


def main():
    options = parse_arguments()
    Execute(options)


if __name__ == "__main__":
    main()

#!/bin/python

"""

straintables' main pipeline script;


"""

import os
import argparse
import shutil
import straintables
import subprocess

from Bio.Align.Applications import ClustalOmegaCommandline

from straintables.logo import logo

from straintables.Executable import primerFinder, detectMutations,\
    compareHeatmap, matrixAnalysis

from straintables.Database import directoryManager

Description = """

Main straintables pipeline.
Will initialize an analysis directory based on the provided genomes,
annotation and wanted regions."
If primers were not declared at the wanted regions file,
it will try to create primers based on the region sequence,
by using the region boundaries defined at the annotation file.

The resulting directory can be inspected manually
or used to build dissimilarity matrices through the command 'stview'.

"""


class Options():
    def __init__(self, options):
        self.__dict__.update(options)


def find_primers(options):

    return primerFinder.Execute(options)


def run_alignment(filePrefix,
                  clustalPath=straintables.Definitions.ClustalCommand):
    infile = filePrefix + ".fasta"
    outfile = filePrefix + ".aln"

    aln_cmd = ClustalOmegaCommandline(clustalPath,
                                      infile=infile,
                                      outfile=outfile,
                                      force=True,
                                      outfmt="clustal")
    stdout, stderr = aln_cmd()

    print(stdout)


def draw_tree(filePrefix):
    infile = filePrefix + ".ph"
    outfile = filePrefix + "pdf"

    treeOptions = Options({
        "InputFile": infile,
        "OutputFile": outfile
    })

    straintables.DrawGraphics.drawTree.Execute(treeOptions)


def run_meshclust(filePrefix):
    subprocess.run([
        "meshclust",
        filePrefix + ".fasta",
        "--output",
        filePrefix + ".clst",
        "--id", "0.999",
        "--align"
    ])


def detect_mutations(filePrefix):
    infile = filePrefix + ".aln"

    mutationsOptions = Options({
        "InputFile": infile,
        "PlotSubtitle": ""
    })

    detectMutations.Execute(mutationsOptions)


def matrix_analysis(WorkingDirectory):
    analysisOptions = Options({
        "WorkingDirectory": WorkingDirectory,
        "updateOnly": False
    })

    return matrixAnalysis.Execute(analysisOptions)


def parse_arguments():
    parser = argparse.ArgumentParser(description=Description)

    parser.add_argument("--noamplicon", dest="DoAmplicon",
                        action="store_false", default=True)

    parser.add_argument("--noalign", dest="DoAlignment",
                        action="store_false", default=True)

    parser.add_argument("--alnmode", dest="AlignmentMode",
                        default="clustal")

    parser.add_argument("--clustalpath", dest="ClustalPath",
                        default=straintables.Definitions.ClustalCommand)

    parser = primerFinder.parse_arguments(parser)

    return parser.parse_args()


def TestMeshclust():
    # -- TEST MESHCLUST SETUP;
    if shutil.which("meshclust"):
        print("MeshClust enabled!")
        return True
    else:
        print("MeshClust not found! Disabled...")
        return False


def process_individual_region(options, locusName, MeshClustEnabled):
    filePrefix = os.path.join(
        options.WorkingDirectory,
        straintables.Definitions.FastaRegionPrefix + locusName)

    print("Running alignment for %s..." % locusName)

    run_alignment(filePrefix,
                  clustalPath=options.ClustalPath)

    # draw_tree(filePrefix)
    detect_mutations(filePrefix)
    if MeshClustEnabled:
        run_meshclust(filePrefix)


def Execute(options):

    if not options.PrimerFile:
        print("Fatal: No primer file specified!")
        exit(1)

    # -- SELECT WORKING DIRECTORY;
    if not options.WorkingDirectory:
        AnalysisCode = os.path.splitext(options.PrimerFile)[0]
        AnalysisCode = os.path.basename(AnalysisCode)

        WorkingDirectoryBase = "analysisResults"
        options.WorkingDirectory = os.path.join(WorkingDirectoryBase,
                                                AnalysisCode)

    # -- TEST CLUSTAL SETUP;
    if not shutil.which(options.ClustalPath):
        print("%s not found! Aborting..." % options.ClustalPath)
        exit(1)

    MeshClustEnabled = TestMeshclust()
    directoryManager.createDirectoryPath(options.WorkingDirectory)

    # SHOW BEAUTIFUL ASCII ART;
    print(logo)

    # -- RUN PIPELINE;
    if options.DoAmplicon:
        result = find_primers(options)
        if not result:
            print("Failure to find primers.")
            exit(1)

    AllowedAlignModes = ["clustal"]
    if options.AlignmentMode not in AllowedAlignModes:
        print("Unknown alignment mode %s." % (options.AlignmentMode))
        exit(1)

    MatchedRegions = straintables.OutputFile.MatchedRegions(
        options.WorkingDirectory)
    MatchedRegions.read()

    SuccessfulLoci = MatchedRegions.content["LocusName"]

    if options.DoAlignment:
        for locusName in SuccessfulLoci:
            process_individual_region(options, locusName, MeshClustEnabled)

    if matrix_analysis(options.WorkingDirectory):
        print("Analysis successful.")


def main():
    options = parse_arguments()
    Execute(options)


if __name__ == "__main__":
    main()

#!/bin/python straintables' main pipeline script; Main straintables pipeline. Will initialize an analysis directory based on the provided genomes, annotation and wanted regions." If primers were not declared at the wanted regions file, it will try to create primers based on the region sequence, by using the region boundaries defined at the annotation file.  The resulting directory can be inspected manually or used to build dissimilarity matrices through the command 'stview'. # -- TEST MESHCLUST SETUP; # draw_tree(filePrefix) # -- SELECT WORKING DIRECTORY; # -- TEST CLUSTAL SETUP; # SHOW BEAUTIFUL ASCII ART; # -- RUN PIPELINE;