__author__ = "Johannes Köster"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=True, stderr=True)

## Extract arguments
extra = snakemake.params.get("extra", "")

shell("bcftools index {extra} {snakemake.input[0]} {log}")

__author__ = "William Rowell"
__copyright__ = "Copyright 2020, William Rowell"
__email__ = "[email protected]"
__license__ = "MIT"

import sys
from snakemake.shell import shell

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

bed = snakemake.input.get("bed", "")
by = snakemake.params.get("by", "")
if by:
    if bed:
        sys.exit(
            "Either provide a bed input file OR a window size via params.by, not both."
        )
    else:
        by = f"--by {by}"
if bed:
    by = f"--by {bed}"

quantize_out = False
thresholds_out = False
regions_bed_out = False
region_dist_out = False
for file in snakemake.output:
    if ".per-base." in file and "--no-per-base" in extra:
        sys.exit(
            "You asked not to generate per-base output (--no-per-base), but your rule specifies a '.per-base.' output file. Remove one of the two."
        )
    if ".quantized.bed.gz" in file:
        quantize_out = True
    if ".thresholds.bed.gz" in file:
        thresholds_out = True
    if ".mosdepth.region.dist.txt" in file:
        region_dist_out = True
    if ".regions.bed.gz" in file:
        regions_bed_out = True


if by and not regions_bed_out:
    sys.exit(
        "You ask for by-region output. Please also specify *.regions.bed.gz as a rule output."
    )

if by and not region_dist_out:
    sys.exit(
        "You ask for by-region output. Please also specify *.mosdepth.region.dist.txt as a rule output."
    )

if (region_dist_out or regions_bed_out) and not by:
    sys.exit(
        "You specify *.regions.bed.gz and/or *.mosdepth.region.dist.txt as a rule output. You also need to ask for by-region output via 'input.bed' or 'params.by'."
    )

quantize = snakemake.params.get("quantize", "")
if quantize:
    if not quantize_out:
        sys.exit(
            "You ask for quantized output via params.quantize. Please also specify *.quantized.bed.gz as a rule output."
        )
    quantize = f"--quantize {quantize}"

if not quantize and quantize_out:
    sys.exit(
        "The rule has output *.quantized.bed.gz specified. Please also specify params.quantize to actually generate it."
    )


thresholds = snakemake.params.get("thresholds", "")
if thresholds:
    if not thresholds_out:
        sys.exit(
            "You ask for --thresholds output via params.thresholds. Please also specify *.thresholds.bed.gz as a rule output."
        )
    thresholds = f"--thresholds {thresholds}"

if not thresholds and thresholds_out:
    sys.exit(
        "The rule has output *.thresholds.bed.gz specified. Please also specify params.thresholds to actually generate it."
    )


precision = snakemake.params.get("precision", "")
if precision:
    precision = f"MOSDEPTH_PRECISION={precision}"


fasta = snakemake.input.get("fasta", "")
if fasta:
    fasta = f"--fasta {fasta}"


# mosdepth takes additional threads through its option --threads
# One thread for mosdepth
# Other threads are *additional* decompression threads passed to the '--threads' argument
threads = "" if snakemake.threads <= 1 else "--threads {}".format(snakemake.threads - 1)


# named output summary = "*.mosdepth.summary.txt" is required
prefix = snakemake.output.summary.replace(".mosdepth.summary.txt", "")


shell(
    "({precision} mosdepth {threads} {fasta} {by} {quantize} {thresholds} {extra} {prefix} {snakemake.input.bam}) {log}"
)

__author__ = "Johannes Köster, Christopher Schröder"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"


import tempfile
from snakemake.shell import shell
from snakemake_wrapper_utils.java import get_java_opts

log = snakemake.log_fmt_shell()

extra = snakemake.params.get("extra", "")
java_opts = get_java_opts(snakemake)

bams = snakemake.input.bams
if isinstance(bams, str):
    bams = [bams]
bams = list(map("--INPUT {}".format, bams))

if snakemake.output.bam.endswith(".cram"):
    output = "/dev/stdout"
    if snakemake.params.embed_ref:
        view_options = "-O cram,embed_ref"
    else:
        view_options = "-O cram"
    convert = f" | samtools view -@ {snakemake.threads} {view_options} --reference {snakemake.input.ref} -o {snakemake.output.bam}"
else:
    output = snakemake.output.bam
    convert = ""

with tempfile.TemporaryDirectory() as tmpdir:
    shell(
        "(picard MarkDuplicates"  # Tool and its subcommand
        " {java_opts}"  # Automatic java option
        " {extra}"  # User defined parmeters
        " {bams}"  # Input bam(s)
        " --TMP_DIR {tmpdir}"
        " --OUTPUT {output}"  # Output bam
        " --METRICS_FILE {snakemake.output.metrics}"  # Output metrics
        " {convert} ) {log}"  # Logging
    )

__author__ = "Patrik Smeds"
__copyright__ = "Copyright 2016, Patrik Smeds"
__email__ = "[email protected]"
__license__ = "MIT"

from os.path import splitext

from snakemake.shell import shell

log = snakemake.log_fmt_shell(stdout=False, stderr=True)

# Check inputs/arguments.
if len(snakemake.input) == 0:
    raise ValueError("A reference genome has to be provided!")
elif len(snakemake.input) > 1:
    raise ValueError("Only one reference genome can be inputed!")

# Prefix that should be used for the database
prefix = snakemake.params.get("prefix", splitext(snakemake.output.idx[0])[0])

if len(prefix) > 0:
    prefix = "-p " + prefix

# Contrunction algorithm that will be used to build the database, default is bwtsw
construction_algorithm = snakemake.params.get("algorithm", "")

if len(construction_algorithm) != 0:
    construction_algorithm = "-a " + construction_algorithm

shell(
    "bwa index" " {prefix}" " {construction_algorithm}" " {snakemake.input[0]}" " {log}"
)

__author__ = "Johannes Köster, Julian de Ruiter"
__copyright__ = "Copyright 2016, Johannes Köster and Julian de Ruiter"
__email__ = "[email protected], [email protected]"
__license__ = "MIT"


from os import path
import re
import tempfile
from snakemake.shell import shell


# Extract arguments.
extra = snakemake.params.get("extra", "")

sort = snakemake.params.get("sorting", "none")
sort_order = snakemake.params.get("sort_order", "coordinate")
sort_extra = snakemake.params.get("sort_extra", "")

index = snakemake.input.idx
if isinstance(index, str):
    index = path.splitext(snakemake.input.idx)[0]
else:
    index = path.splitext(snakemake.input.idx[0])[0]


if re.search(r"-T\b", sort_extra) or re.search(r"--TMP_DIR\b", sort_extra):
    sys.exit(
        "You have specified temp dir (`-T` or `--TMP_DIR`) in params.sort_extra; this is automatically set from params.tmp_dir."
    )

log = snakemake.log_fmt_shell(stdout=False, stderr=True)


# Check inputs/arguments.
if not isinstance(snakemake.input.reads, str) and len(snakemake.input.reads) not in {
    1,
    2,
}:
    raise ValueError("input must have 1 (single-end) or " "2 (paired-end) elements")

if sort_order not in {"coordinate", "queryname"}:
    raise ValueError("Unexpected value for sort_order ({})".format(sort_order))

# Determine which pipe command to use for converting to bam or sorting.
if sort == "none":

    # Simply convert to bam using samtools view.
    pipe_cmd = "samtools view -Sbh -o {snakemake.output[0]} -"

elif sort == "samtools":

    # Add name flag if needed.
    if sort_order == "queryname":
        sort_extra += " -n"

    # Sort alignments using samtools sort.
    pipe_cmd = "samtools sort -T {tmp} {sort_extra} -o {snakemake.output[0]} -"

elif sort == "picard":

    # Sort alignments using picard SortSam.
    pipe_cmd = (
        "picard SortSam {sort_extra} --INPUT /dev/stdin"
        " --OUTPUT {snakemake.output[0]} --SORT_ORDER {sort_order} --TMP_DIR {tmp}"
    )

else:
    raise ValueError("Unexpected value for params.sort ({})".format(sort))

with tempfile.TemporaryDirectory() as tmp:
    shell(
        "(bwa mem"
        " -t {snakemake.threads}"
        " {extra}"
        " {index}"
        " {snakemake.input.reads}"
        " | " + pipe_cmd + ") {log}"
    )

shell:
    "rtg format --output {output} {input.genome} &> {log}"

from collections import defaultdict
import sys, os

# sys.path.insert(0, os.path.dirname(__file__))
sys.stderr = open(snakemake.log[0], "w")

from abc import ABC, abstractmethod
from enum import Enum
import pandas as pd
import pysam

from common.classification import CompareExactGenotype, CompareExistence, Class


class Classifications:
    def __init__(self, comparator):
        self.tp_query = 0
        self.tp_truth = 0
        self.fn = 0
        self.fp = 0
        self.comparator = comparator

    def register(self, record):
        for c in self.comparator.classify(record):
            if c.cls is Class.TP_truth:
                self.tp_truth += 1
            elif c.cls is Class.TP_query:
                self.tp_query += 1
            elif c.cls is Class.FN:
                self.fn += 1
            elif c.cls is Class.FP:
                self.fp += 1
            else:
                assert False, "unexpected case"

    def precision(self):
        p = self.tp_query + self.fp
        if p == 0:
            return 1.0
        return float(self.tp_query) / float(p)

    def recall(self):
        t = self.tp_truth + self.fn
        if t == 0:
            return 1.0
        return float(self.tp_truth) / float(t)


def collect_results(vartype):
    classifications_exact = Classifications(CompareExactGenotype(vartype))
    classifications_existence = Classifications(CompareExistence(vartype))

    for record in pysam.VariantFile(snakemake.input.calls):
        classifications_exact.register(record)
        classifications_existence.register(record)

    vartype = "indels" if vartype == "INDEL" else "snvs"

    mismatched_genotype = (
        classifications_existence.tp_query - classifications_exact.tp_query
    )
    if classifications_existence.tp_query > 0:
        mismatched_genotype_rate = (
            mismatched_genotype / classifications_existence.tp_query
        )
    else:
        mismatched_genotype_rate = 0.0

    d = pd.DataFrame(
        {
            "precision": [classifications_existence.precision()],
            "tp_query": [classifications_existence.tp_query],
            "fp": [classifications_existence.fp],
            "recall": [classifications_existence.recall()],
            "tp_truth": [classifications_existence.tp_truth],
            "fn": [classifications_existence.fn],
            "genotype_mismatch_rate": [mismatched_genotype_rate],
        }
    )
    return d[
        [
            "precision",
            "tp_query",
            "fp",
            "recall",
            "tp_truth",
            "fn",
            "genotype_mismatch_rate",
        ]
    ]


assert snakemake.wildcards.vartype in ["snvs", "indels"]
vartype = "SNV" if snakemake.wildcards.vartype == "snvs" else "INDEL"

collect_results(vartype).to_csv(snakemake.output[0], sep="\t", index=False)

import os
import sys

sys.stderr = open(snakemake.log[0], "w")

import pandas as pd
from scipy.cluster.hierarchy import ward, leaves_list
from scipy.spatial.distance import pdist
from sklearn.feature_selection import chi2
from statsmodels.stats.multitest import fdrcorrection
import numpy as np


def collect_chromosomes(f):
    d = pd.read_csv(f, sep="\t", dtype=str, usecols=["chromosome"]).drop_duplicates()
    return d["chromosome"].tolist()


def read_data(f, callset, chromosome=None):
    print("reading", f, "...", file=sys.stderr)
    data = pd.read_csv(
        f,
        sep="\t",
        dtype=str,
    )

    if chromosome is not None:
        data = data.loc[data["chromosome"] == chromosome]
    print(data.head(), file=sys.stderr)

    data = data.set_index(
        [
            "chromosome",
            "position",
            "ref_allele",
            "alt_allele",
            "true_genotype",
        ]
    )
    data.drop("class", axis="columns", inplace=True)

    assert (
        not data.index.duplicated().any()
    ), f"bug: not expecting any duplicates in FP/FN table {f}"

    data.columns = [callset]

    if snakemake.wildcards.classification == "fn":
        data.loc[:, callset] = "FN"
    return data


def get_idx_sorted_by_clustering(data):
    cluster_matrix = ward(pdist(~data.isna(), metric="hamming"))
    idx = leaves_list(cluster_matrix)
    return idx


chromosomes = sorted(
    {chrom for f in snakemake.input.tables for chrom in collect_chromosomes(f)}
)

if not chromosomes:
    chromosomes = [None]

n_written = 0

# process data for each chromosome separately and append to the same files
for i, chromosome in enumerate(chromosomes):
    if n_written > snakemake.params.max_entries:
        break

    data = pd.concat(
        [
            read_data(f, callset, chromosome)
            for f, callset in zip(snakemake.input.tables, snakemake.params.callsets)
        ],
        axis="columns",
    )

    data = data.loc[data.isna().sum(axis="columns").sort_values().index,]

    data = data.dropna(how="all")

    if not data.empty:
        idx_rows = get_idx_sorted_by_clustering(data)
        idx_cols = get_idx_sorted_by_clustering(data.T)
        data = data.iloc[idx_rows, idx_cols]

    label_df = pd.DataFrame(snakemake.params.labels)

    def store(data, output, label_idx=None):
        _label_df = label_df
        if label_idx is not None:
            _label_df = label_df.iloc[[label_idx]]

        # add labels
        index_cols = data.index.names
        cols = data.columns
        data = pd.concat([_label_df, data.reset_index()]).set_index(index_cols)
        # restore column order
        data = data[cols]

        if i == 0:
            mode = "w"
            header = True
        else:
            mode = "a"
            header = False
        data.to_csv(output, sep="\t", mode=mode, header=header)

    store(data, snakemake.output.main)
    n_written += len(data)

    label_df.index = snakemake.params.label_names

    os.makedirs(snakemake.output.dependency_sorting, exist_ok=True)

    # for each label, calculate mutual information and sort FP/FN entries in descending order
    for label_idx, label in enumerate(snakemake.params.label_names):
        outdata = data
        if not data.empty:
            # oe = OrdinalEncoder()
            # le = LabelEncoder()
            # feature matrix: genotypes, transposed into samples x features, replace NA with False (match)
            # and any genotype with True (mismatch with truth).
            feature_matrix = data.reset_index(drop=True).T.copy()
            feature_matrix[~pd.isna(feature_matrix)] = True
            feature_matrix[pd.isna(feature_matrix)] = False

            # target vector: label values, converted into factors
            target_vector = label_df.loc[label]

            # ignore any NA in the target vector and correspondingly remove the rows in the feature matrix
            not_na_target_vector = target_vector[~pd.isna(target_vector)]
            feature_matrix = feature_matrix.loc[not_na_target_vector.index]

            # perfom chi² test against each feature
            _, pvals = chi2(feature_matrix, not_na_target_vector)
            sorted_idx = np.argsort(pvals)

            _, fdr = fdrcorrection(
                pvals, method="negcorr"
            )  # use Benjamini/Yekutieli as variants might be both positively or negatively correlated

            # clone data
            sorted_data = data.copy(deep=True)

            # sort by label
            sorted_target_vector = target_vector.sort_values()
            sorted_data = sorted_data[sorted_target_vector.index]

            # add pvalue and FDR
            sorted_data.insert(0, "FDR dependency", np.around(fdr, 3))
            sorted_data.insert(0, "p-value dependency", np.around(pvals, 3))

            outdata = sorted_data.iloc[sorted_idx]

            # only keep the rather significant entries (but be a bit more permissive than 0.05)
            outdata = outdata.loc[outdata["p-value dependency"] <= 0.25]

        outpath = os.path.join(snakemake.output.dependency_sorting, f"{label}.tsv")
        store(outdata, outpath, label_idx=label_idx)

import sys

sys.stderr = open(snakemake.log[0], "w")

import json
from pysam import VariantFile


with VariantFile(snakemake.input[0]) as infile, open(
    snakemake.output[0], "w"
) as outfile:
    json.dump({"isempty": not any(infile)}, outfile)