comparison data_manager/add_ctat_resource_lib.py @ 32:9b7dc7d09fda draft

Fixing some indentation errors in build_the_library.

31:0df7a729910d

    else:
        print "gmap_the_library(): This code should never be printed. Something is wrong."
    return


def build_the_library(genome_source_directory, genome_build_directory, force_new_build, gmap_build):
    """ genome_source_directory is the location of the source_data needed to build the library.
        Normally it is fully specified, but could be relative.
        genome_build_directory is the location where the library will be built.
        It can be relative to the current working directory or an absolute path.
        build specifies whether to run prep_genome_lib.pl even if it was run before.

            # Create the gmap success file.
            gmap_success_filename = "{:s}.{:s}".format(src_filename, _GmapSuccessFile)
            gmap_success_full_file_path = os.path.join(cannonical_destination, gmap_success_filename)
            create_success_file(gmap_success_full_file_path, \
                                "gmap of:\n\t{:s}\nsucceeded.".format(cannonical_destination))
        elif (build_success_filename in files_in_sourcedir):
            print "The build success file exists, so no build is being attempted:"
            print "\t{:s}".format(build_success_file_path)
            print "Remove the file or set <force new build> if you want a new build to occur."
        if gmap_build:
            print "Checking if we need to gmap the library."
            gmap_the_library(cannonical_destination, force_new_build)
            # gmap_the_library creates a gmap success file if it succeeds.
        else:
            print "build_the_library(): This code should never be printed. Something is wrong."
    return
	# End of build_the_library()

def find_path_to_mutation_lib_integration():
    # We are assuming that we exist inside of a conda environment and that the directory that we want

32:9b7dc7d09fda

    else:
        print "gmap_the_library(): This code should never be printed. Something is wrong."
    return


def build_the_library(genome_source_directory, genome_build_directory, force_new_build=False, gmap_build=False):
    """ genome_source_directory is the location of the source_data needed to build the library.
        Normally it is fully specified, but could be relative.
        genome_build_directory is the location where the library will be built.
        It can be relative to the current working directory or an absolute path.
        build specifies whether to run prep_genome_lib.pl even if it was run before.

            # Create the gmap success file.
            gmap_success_filename = "{:s}.{:s}".format(src_filename, _GmapSuccessFile)
            gmap_success_full_file_path = os.path.join(cannonical_destination, gmap_success_filename)
            create_success_file(gmap_success_full_file_path, \
                                "gmap of:\n\t{:s}\nsucceeded.".format(cannonical_destination))
    elif (build_success_filename in files_in_sourcedir):
        print "The build success file exists, so no build is being attempted:"
        print "\t{:s}".format(build_success_file_path)
        print "Remove the file or set <force new build> if you want a new build to occur."
        # We might still need to do a gmap_build.
        if gmap_build:
            print "Checking if we need to gmap the library."
            gmap_the_library(cannonical_destination, force_new_build)
            # gmap_the_library creates a gmap success file if it succeeds.
    else:
        print "build_the_library(): This code should never be printed. Something is wrong."

    return
	# End of build_the_library()

def find_path_to_mutation_lib_integration():
    # We are assuming that we exist inside of a conda environment and that the directory that we want