""" MultiQC submodule to parse output from Picard RnaSeqMetrics """

import logging
import os
import re
from collections import OrderedDict

from multiqc.plots import bargraph, linegraph

# Initialise the logger
log = logging.getLogger(__name__)


def parse_reports(self):
    """Find Picard RnaSeqMetrics reports and parse their data"""

    # Set up vars
    self.picard_RnaSeqMetrics_data = dict()
    self.picard_RnaSeqMetrics_histogram = dict()

    # Go through logs and find Metrics
    for f in self.find_log_files("picard/rnaseqmetrics", filehandles=True):
        s_name = None
        in_hist = False
        for l in f["f"]:
            # Catch the histogram values
            if s_name is not None and in_hist is True:
                try:
                    sections = l.split("\t")
                    pos = int(sections[0])
                    coverage = float(sections[1])
                    self.picard_RnaSeqMetrics_histogram[s_name][pos] = coverage
                except ValueError:
                    # Reset in case we have more in this log file
                    s_name = None
                    in_hist = False

            # New log starting
            if "rnaseqmetrics" in l.lower() and "INPUT" in l:
                s_name = None
                # Pull sample name from input
                fn_search = re.search(r"INPUT(?:=|\s+)(\[?[^\s]+\]?)", l, flags=re.IGNORECASE)
                if fn_search:
                    s_name = os.path.basename(fn_search.group(1).strip("[]"))
                    s_name = self.clean_s_name(s_name, f)

            if s_name is not None:
                if "rnaseqmetrics" in l.lower() and "## METRICS CLASS" in l:
                    if s_name in self.picard_RnaSeqMetrics_data:
                        log.debug("Duplicate sample name found in {}! Overwriting: {}".format(f["fn"], s_name))
                    self.picard_RnaSeqMetrics_data[s_name] = dict()
                    self.picard_RnaSeqMetrics_histogram[s_name] = dict()
                    self.add_data_source(f, s_name, section="RnaSeqMetrics")
                    keys = f["f"].readline().strip("\n").split("\t")
                    vals = f["f"].readline().strip("\n").split("\t")
                    for i, k in enumerate(keys):
                        # Multiply percentages by 100
                        if k.startswith("PCT_"):
                            try:
                                vals[i] = float(vals[i]) * 100.0
                            except (ValueError, IndexError):
                                pass
                        # Save the key:value pairs
                        try:
                            self.picard_RnaSeqMetrics_data[s_name][k] = float(vals[i])
                        except ValueError:
                            self.picard_RnaSeqMetrics_data[s_name][k] = vals[i]
                        except IndexError:
                            pass  # missing data
                    # Calculate some extra numbers
                    if "PF_BASES" in keys and "PF_ALIGNED_BASES" in keys:
                        self.picard_RnaSeqMetrics_data[s_name]["PF_NOT_ALIGNED_BASES"] = (
                            self.picard_RnaSeqMetrics_data[s_name]["PF_BASES"]
                            - self.picard_RnaSeqMetrics_data[s_name]["PF_ALIGNED_BASES"]
                        )

            if s_name is not None and "normalized_position	All_Reads.normalized_coverage" in l:
                self.picard_RnaSeqMetrics_histogram[s_name] = dict()
                in_hist = True

        for key in list(self.picard_RnaSeqMetrics_data.keys()):
            if len(self.picard_RnaSeqMetrics_data[key]) == 0:
                self.picard_RnaSeqMetrics_data.pop(key, None)
        for s_name in list(self.picard_RnaSeqMetrics_histogram.keys()):
            if len(self.picard_RnaSeqMetrics_histogram[s_name]) == 0:
                self.picard_RnaSeqMetrics_histogram.pop(s_name, None)
                log.debug("Ignoring '{}' histogram as no data parsed".format(s_name))

            # Superfluous function call to confirm that it is used in this module
            # Replace None with actual version if it is available
            self.add_software_version(None, s_name)

    # Filter to strip out ignored sample names
    self.picard_RnaSeqMetrics_data = self.ignore_samples(self.picard_RnaSeqMetrics_data)

    if len(self.picard_RnaSeqMetrics_data) > 0:
        # Write parsed data to a file
        self.write_data_file(self.picard_RnaSeqMetrics_data, "multiqc_picard_RnaSeqMetrics")

        # Add to general stats table
        GenStatsHeaders = OrderedDict()
        GenStatsHeaders["PCT_RIBOSOMAL_BASES"] = {
            "title": "% rRNA",
            "description": "Percent of aligned bases overlapping ribosomal RNA regions",
            "max": 100,
            "min": 0,
            "suffix": "%",
            "scale": "Reds",
        }
        GenStatsHeaders["PCT_MRNA_BASES"] = {
            "title": "% mRNA",
            "description": "Percent of aligned bases overlapping UTRs and coding regions of mRNA transcripts",
            "max": 100,
            "min": 0,
            "suffix": "%",
            "scale": "Greens",
        }
        self.general_stats_addcols(self.picard_RnaSeqMetrics_data, GenStatsHeaders)

        # Bar plot of bases assignment
        bg_cats = OrderedDict()
        bg_cats["CODING_BASES"] = {"name": "Coding"}
        bg_cats["UTR_BASES"] = {"name": "UTR"}
        bg_cats["INTRONIC_BASES"] = {"name": "Intronic"}
        bg_cats["INTERGENIC_BASES"] = {"name": "Intergenic"}
        bg_cats["RIBOSOMAL_BASES"] = {"name": "Ribosomal"}
        bg_cats["PF_NOT_ALIGNED_BASES"] = {"name": "PF not aligned"}

        # Warn user if any samples are missing 'RIBOSOMAL_BASES' data; ie picard was run without an rRNA interval file.
        warn_rrna = ""
        rrna_missing = []
        for s_name, metrics in self.picard_RnaSeqMetrics_data.items():
            if metrics["RIBOSOMAL_BASES"] == "":
                rrna_missing.append(s_name)
        if len(rrna_missing):
            if len(rrna_missing) < 5:
                missing_samples = "for samples <code>{}</code>".format("</code>, <code>".join(rrna_missing))
            else:
                missing_samples = "<strong>{} samples</strong>".format(len(rrna_missing))
            warn_rrna = """
            <div class="alert alert-warning">
              <span class="glyphicon glyphicon-warning-sign"></span>
              Picard was run without an rRNA annotation file {}, therefore the ribosomal assignment is not available. To correct, rerun with the <code>RIBOSOMAL_INTERVALS</code> parameter, as documented <a href="https://broadinstitute.github.io/picard/command-line-overview.html#CollectRnaSeqMetrics" target="_blank">here</a>.
            </div>
            """.format(
                missing_samples
            )

        pconfig = {
            "id": "picard_rnaseqmetrics_assignment_plot",
            "title": "Picard: RnaSeqMetrics Base Assignments",
            "ylab": "Number of bases",
        }
        self.add_section(
            name="RnaSeqMetrics Assignment",
            anchor="picard-rna-assignment",
            description="Number of bases in primary alignments that align to regions in the reference genome."
            + warn_rrna,
            plot=bargraph.plot(self.picard_RnaSeqMetrics_data, bg_cats, pconfig),
        )

        # Bar plot of strand mapping
        bg_cats = OrderedDict()
        bg_cats["CORRECT_STRAND_READS"] = {"name": "Correct"}
        bg_cats["INCORRECT_STRAND_READS"] = {"name": "Incorrect", "color": "#8e123c"}

        pdata = dict()
        for s_name, d in self.picard_RnaSeqMetrics_data.items():
            if d["CORRECT_STRAND_READS"] > 0 and d["INCORRECT_STRAND_READS"] > 0:
                pdata[s_name] = d
        if len(pdata) > 0:
            pconfig = {
                "id": "picard_rnaseqmetrics_strand_plot",
                "title": "Picard: RnaSeqMetrics Strand Mapping",
                "ylab": "Number of reads",
                "hide_zero_cats": False,
            }
            self.add_section(
                name="RnaSeqMetrics Strand Mapping",
                anchor="picard-rna-strand",
                description="Number of aligned reads that map to the correct strand.",
                plot=bargraph.plot(self.picard_RnaSeqMetrics_data, bg_cats, pconfig),
            )

        # Section with histogram plot
        if len(self.picard_RnaSeqMetrics_histogram) > 0:
            # Plot the data and add section
            pconfig = {
                "smooth_points": 500,
                "smooth_points_sumcounts": [True, False],
                "id": "picard_rna_coverage",
                "title": "Picard: Normalized Gene Coverage",
                "ylab": "Coverage",
                "xlab": "Percent through gene",
                "xDecimals": False,
                "tt_label": "<b>{point.x}%</b>: {point.y:.0f}",
                "ymin": 0,
            }
            self.add_section(
                name="Gene Coverage",
                anchor="picard-rna-coverage",
                plot=linegraph.plot(self.picard_RnaSeqMetrics_histogram, pconfig),
            )

    # Return the number of detected samples to the parent module
    return len(self.picard_RnaSeqMetrics_data)
