#!/usr/bin/env python

import argparse
import logging
import os

# Create a logger
logging.basicConfig(format='%(name)s - %(asctime)s %(levelname)s: %(message)s')
logger = logging.getLogger(__file__)
logger.setLevel(logging.INFO)

mqc_main = """#id: 'biotype-gs'
#plot_type: 'generalstats'
#pconfig:"""

mqc_pconf="""#    percent_{ft}:
#        title: '% {ft}'
#        namespace: 'Biotype Counts'
#        description: '% reads overlapping {ft} features'
#        max: 100
#        min: 0
#        scale: 'RdYlGn-rev'
#        format: '{{:.2f}}%'"""

def mqc_feature_stat(bfile, features, outfile, sname=None):

    # If sample name not given use file name
    if not sname:
        sname = os.path.splitext(os.path.basename(bfile))[0]

    # Try to parse and read biocount file
    fcounts = {}
    try:
        with open(bfile, 'r') as bfl:
            for ln in bfl:
                if ln.startswith('#'):
                    continue
                ft, cn = ln.strip().split('\t')
                fcounts[ft] = float(cn)
    except:
        logger.error("Trouble reading the biocount file {}".format(bfile))
        return

    total_count = sum(fcounts.values())
    if total_count == 0:
        logger.error("No biocounts found, exiting")
        return

    # Calculate percentage for each requested feature
    fpercent = {f: (fcounts[f]/total_count)*100 for f in features if f in fcounts}
    if len(fpercent) == 0:
        logger.error("Any of given features '{}' not found in the biocount file".format(", ".join(features), bfile))
        return

    # Prepare the output strings
    out_head, out_value, out_mqc = ("Sample", sname, mqc_main)
    for ft, pt in fpercent.items():
        out_head = "{}\tpercent_{}".format(out_head, ft)
        out_value = "{}\t{}".format(out_value, pt)
        out_mqc = "{}\n{}".format(out_mqc, mqc_pconf.format(ft=ft))

    # Write the output to a file
    with open(outfile, 'w') as ofl:
        out_final = "\n".join([out_mqc, out_head, out_value]).strip()
        ofl.write(out_final + "\n")

if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="""Calculate features percentage for biotype counts""")
    parser.add_argument("biocount", type=str, help="File with all biocounts")
    parser.add_argument("-f", "--features", dest='features', required=True, nargs='+', help="Features to count")
    parser.add_argument("-s", "--sample", dest='sample', type=str, help="Sample Name")
    parser.add_argument("-o", "--output", dest='output', default='biocount_percent.tsv', type=str, help="Sample Name")
    args = parser.parse_args()
    mqc_feature_stat(args.biocount, args.features, args.output, args.sample)


@@ -1632,21 +1632,36 @@
 ample%22, 
+%22'%7B%7D'%22.format(
 sname
+)
 , mqc_ma
@@ -2690,9 +2690,8 @@
 sample)%0A
-%0A

Use quotes for feature counts in MultiQC