# Path: diagnostic_primers/primersearch.py
# def build_commands(collection, primersearch_dir, mismatchpercent, existingfiles):
# def build_command(primerfile, seqfile, filestem, mismatchpercent):
#     def __init__(self, name):
#     def add_amplimer(self, amplimer):
#     def name(self):
#     def amplimers(self):
#     def __str__(self):
#     def __init__(self, name):
#     def name(self):
#     def fwd(self):
#     def fwd(self, val):
#     def rev(self):
#     def rev(self, val):
#     def sequence(self):
#     def sequence(self, val):
#     def length(self):
#     def length(self, val):
#     def __len__(self):
#     def __str__(self):
#     def default(self, o):  # pylint: disable=E0202
#     def __init__(self, name):
#     def add_amplimer(self, amplimer, targetname):
#     def from_json(self, filename):
#     def filter_primers(self, primers):
#     def get_target_amplimers(self, target):
#     def split_on_targets(self):
#     def write_json(self, outfilename):
#     def write_bed(self, outdir):
#     def write_target_bed(self, target, outfname):
#     def targets(self):
#     def targets(self, tgtdict):
#     def default(self, o):  # pylint: disable=E0202
# def parse_output(filename, genomepath):
# def load_collection_amplicons(coll):
# class PrimerSearchRecord:
# class PrimerSearchAmplimer:
# class AmplimersEncoder(json.JSONEncoder):
# class PDPGenomeAmplicons:
# class PDPGenomeAmpliconsEncoder(json.JSONEncoder):
# 
# Path: diagnostic_primers/config.py
# class ConfigSyntaxError(Exception):
# class PDPCollectionException(PDPException):
# class PDPEncoder(json.JSONEncoder):
# class PDPCollection(object):
# class PDPData(object):
#     def __init__(self, message):
#     def __init__(self, msg="Problem with PDPCollection"):
#     def default(self, obj):
#     def __init__(self, name="pdp.py"):
#     def from_tab(self, filename):
#     def from_json(self, filename):
#     def add_data(
#         self,
#         name=None,
#         groups=None,
#         seqfile=None,
#         filtered_seqfile=None,
#         features=None,
#         primers=None,
#         primersearch=None,
#         target_amplicons=None,
#     ):
#     def write_json(self, outfilename):
#     def write_tab(self, outfilename):
#     def __parse_row(row):
#     def data(self):
#     def groups(self):
#     def get_groupmembers(self, val):
#     def __getitem__(self, key):
#     def __len__(self):
#     def __init__(
#         self,
#         name,
#         groups,
#         seqfile,
#         filtered_seqfile,
#         features,
#         primers,
#         primersearch,
#         target_amplicons,
#     ):
#     def stitch(self, outdir=None):
#     def replace_ambiguities(self, outdir=None):
#     def create_filtered_genome(self, filteredpath, spacerlen, suffix, flanklen=0):
#     def write_primers(self, outfilename, fmt="fasta"):
#     def name(self):
#     def name(self, value):
#     def groups(self):
#     def groups(self, value):
#     def seqfile(self):
#     def seqfile(self, value):
#     def target_amplicons(self):
#     def target_amplicons(self, value):
#     def filtered_seqfile(self):
#     def filtered_seqfile(self, value):
#     def filestem(self):
#     def features(self):
#     def features(self, value):
#     def primers(self):
#     def primers(self, value):
#     def primersearch(self):
#     def primersearch(self, value):
#     def seqnames(self):
#     def needs_stitch(self):
#     def has_ambiguities(self):


import os
import shlex
import shutil
import subprocess
from diagnostic_primers import primersearch, config
from tools import PDPTestCase
        pipe = subprocess.run(
            cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True, shell=False
        )  #  nosec
        # EMBOSS writes information out to STDERR
        self.assertEqual(pipe.stderr[:6], b"EMBOSS")

    def test_primersearch_cmd(self):
        """primersearch command builds correctly."""
        cmd = primersearch.build_command(
            "testfile.ep3",
            "testfile.fas",
            "query_ps_subject.primersearch",
            self.mismatchpercent,
        )
        target = " ".join(
            [
                self.ps_exe,
                "-auto",
                "-outfile=query_ps_subject.primersearch",
                "-seqall=testfile.fas",
                "-infile=testfile.ep3",
                "-mismatchpercent=10",
            ]
        )
        self.assertEqual(str(cmd), target)

    def test_primersearch_cmds(self):
        """primersearch command creation completes with no errors."""
        pdpc = config.PDPCollection()
        pdpc.from_json(self.inconf)

# Path: diagnostic_primers/primersearch.py
# def build_commands(collection, primersearch_dir, mismatchpercent, existingfiles):
# def build_command(primerfile, seqfile, filestem, mismatchpercent):
#     def __init__(self, name):
#     def add_amplimer(self, amplimer):
#     def name(self):
#     def amplimers(self):
#     def __str__(self):
#     def __init__(self, name):
#     def name(self):
#     def fwd(self):
#     def fwd(self, val):
#     def rev(self):
#     def rev(self, val):
#     def sequence(self):
#     def sequence(self, val):
#     def length(self):
#     def length(self, val):
#     def __len__(self):
#     def __str__(self):
#     def default(self, o):  # pylint: disable=E0202
#     def __init__(self, name):
#     def add_amplimer(self, amplimer, targetname):
#     def from_json(self, filename):
#     def filter_primers(self, primers):
#     def get_target_amplimers(self, target):
#     def split_on_targets(self):
#     def write_json(self, outfilename):
#     def write_bed(self, outdir):
#     def write_target_bed(self, target, outfname):
#     def targets(self):
#     def targets(self, tgtdict):
#     def default(self, o):  # pylint: disable=E0202
# def parse_output(filename, genomepath):
# def load_collection_amplicons(coll):
# class PrimerSearchRecord:
# class PrimerSearchAmplimer:
# class AmplimersEncoder(json.JSONEncoder):
# class PDPGenomeAmplicons:
# class PDPGenomeAmpliconsEncoder(json.JSONEncoder):
# 
# Path: diagnostic_primers/config.py
# class ConfigSyntaxError(Exception):
# class PDPCollectionException(PDPException):
# class PDPEncoder(json.JSONEncoder):
# class PDPCollection(object):
# class PDPData(object):
#     def __init__(self, message):
#     def __init__(self, msg="Problem with PDPCollection"):
#     def default(self, obj):
#     def __init__(self, name="pdp.py"):
#     def from_tab(self, filename):
#     def from_json(self, filename):
#     def add_data(
#         self,
#         name=None,
#         groups=None,
#         seqfile=None,
#         filtered_seqfile=None,
#         features=None,
#         primers=None,
#         primersearch=None,
#         target_amplicons=None,
#     ):
#     def write_json(self, outfilename):
#     def write_tab(self, outfilename):
#     def __parse_row(row):
#     def data(self):
#     def groups(self):
#     def get_groupmembers(self, val):
#     def __getitem__(self, key):
#     def __len__(self):
#     def __init__(
#         self,
#         name,
#         groups,
#         seqfile,
#         filtered_seqfile,
#         features,
#         primers,
#         primersearch,
#         target_amplicons,
#     ):
#     def stitch(self, outdir=None):
#     def replace_ambiguities(self, outdir=None):
#     def create_filtered_genome(self, filteredpath, spacerlen, suffix, flanklen=0):
#     def write_primers(self, outfilename, fmt="fasta"):
#     def name(self):
#     def name(self, value):
#     def groups(self):
#     def groups(self, value):
#     def seqfile(self):
#     def seqfile(self, value):
#     def target_amplicons(self):
#     def target_amplicons(self, value):
#     def filtered_seqfile(self):
#     def filtered_seqfile(self, value):
#     def filestem(self):
#     def features(self):
#     def features(self, value):
#     def primers(self):
#     def primers(self, value):
#     def primersearch(self):
#     def primersearch(self, value):
#     def seqnames(self):
#     def needs_stitch(self):
#     def has_ambiguities(self):


# Path: tests/test_primersearch.py
import os
import shlex
import shutil
import subprocess
from diagnostic_primers import primersearch, config
from tools import PDPTestCase

        pipe = subprocess.run(
            cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True, shell=False
        )  #  nosec
        # EMBOSS writes information out to STDERR
        self.assertEqual(pipe.stderr[:6], b"EMBOSS")

    def test_primersearch_cmd(self):
        """primersearch command builds correctly."""
        cmd = primersearch.build_command(
            "testfile.ep3",
            "testfile.fas",
            "query_ps_subject.primersearch",
            self.mismatchpercent,
        )
        target = " ".join(
            [
                self.ps_exe,
                "-auto",
                "-outfile=query_ps_subject.primersearch",
                "-seqall=testfile.fas",
                "-infile=testfile.ep3",
                "-mismatchpercent=10",
            ]
        )
        self.assertEqual(str(cmd), target)

    def test_primersearch_cmds(self):
        """primersearch command creation completes with no errors."""
        pdpc = config.PDPCollection()
        pdpc.from_json(self.inconf)

        primersearch.build_commands(