import argparse
from agutil import status_bar
import subprocess
import csv
import shutil
from qtl.annotation import Annotation
import tempfile

def run(args):
    print("Parsing GTF")
    gtf = Annotation(args.gtf.name)
    print("Parsing GCT")
    numRows = int(subprocess.check_output("wc -l %s" % args.gct.name, shell=True).decode().strip().split()[0]) - 3
    header = ''.join([next(args.gct), next(args.gct)])
    reader = csv.DictReader(args.gct, delimiter='\t')
    w = tempfile.NamedTemporaryFile('w')
    w.write(header)
    writer = csv.DictWriter(w, reader.fieldnames, delimiter='\t', lineterminator='\n')
    writer.writeheader()
    current = None
    features = []
    for line in status_bar.iter(reader, maximum=numRows):
        gene = '_'.join(line['Name'].split('_')[:-1])
        if gene != current:
            if current is not None:
                ref = gtf.get_gene(current)
                try:
                    if len(ref):
                        ref = ref[0]
                except:
                    pass
                exons = {exon.id:exon for transcript in ref.transcripts for exon in transcript.exons}
                raw_size = len(exons)
                for exon in [exon for exon in exons]:
                    try:
                        if exon.isdigit() and int(exon) <= raw_size:
                            exons[current+'_'+exon] = exons[exon]
                    except:
                        pass
                features.sort(
                    key=lambda feat:(
                        1 if exons[feat['Name']].length == 1 else 0,
                        exons[feat['Name']].start_pos,
                        exons[feat['Name']].end_pos
                    )
                )
                for i in range(len(features)):
                    parts = features[i]['Name'].split('_')
                    prefix = '_'.join(parts[:-1])
                    suffix = parts[-1]
                    if exons[features[i]['Name']].length == 1:
                        features[i][reader.fieldnames[-1]] = 0
                    suffix = str(i)
                    features[i]['Name'] = prefix+'_'+suffix
                writer.writerows(features)
            current = gene
            features = []
        features.append({k:v for k,v in line.items()})
    if len(features):
        ref = gtf.get_gene(current)
        try:
            if len(ref):
                ref = ref[0]
        except:
            pass
        exons = {exon.id:exon for transcript in ref.transcripts for exon in transcript.exons}
        raw_size = len(exons)
        for exon in [exon for exon in exons]:
            try:
                if exon.isdigit() and int(exon) <= raw_size:
                    exons[current+'_'+exon] = exons[exon]
            except:
                pass
        features.sort(
            key=lambda feat:(
                1 if exons[feat['Name']].length == 1 else 0,
                exons[feat['Name']].start_pos,
                exons[feat['Name']].end_pos
            )
        )
        for i in range(len(features)):
            prefix, suffix = features[i]['Name'].split('_')
            if exons[features[i]['Name']].length == 1:
                features[i]['Counts'] = 0
            suffix = str(i)
            features[i]['Name'] = prefix+'_'+suffix
            writer.writerows(features)
    print("Cleaning up")
    w.flush()
    args.gct.close()
    shutil.copyfile(
        args.gct.name,
        args.gct.name+'.bak'
    )
    shutil.copyfile(
        w.name,
        args.gct.name
    )


def main():
    parser = argparse.ArgumentParser('flipper')

    parser.add_argument(
        'gct',
        type=argparse.FileType('r'),
        help="RNA-SeQC 2 Exon reads gct file"
    )

    parser.add_argument(
        'gtf',
        type=argparse.FileType('r'),
        help="Reference GTF for the exons"
    )

    args = parser.parse_args()
    run(args)

if __name__ == '__main__':
    main()

import argparse
from agutil import status_bar
import subprocess
import csv
import shutil
from qtl.annotation import Annotation
import tempfile

def run(args):
    print("Parsing GTF")
    gtf = Annotation(args.gtf.name)
    print("Parsing GCT")
    numRows = int(subprocess.check_output("wc -l %s" % args.gct.name, shell=True).decode().strip().split()[0]) - 3
    header = ''.join([next(args.gct), next(args.gct)])
    reader = csv.DictReader(args.gct, delimiter='\t')
    w = tempfile.NamedTemporaryFile('w')
    w.write(header)
    writer = csv.DictWriter(w, reader.fieldnames, delimiter='\t', lineterminator='\n')
    writer.writeheader()
    current = None
    features = []
    for line in status_bar.iter(reader, maximum=numRows):
        gene = '_'.join(line['Name'].split('_')[:-1])
        if gene != current:
            if current is not None:
                ref = gtf.get_gene(current)
                try:
                    if len(ref):
                        ref = ref[0]
                except:
                    pass
                exons = {exon.id:exon for transcript in ref.transcripts for exon in transcript.exons}
                raw_size = len(exons)
                for exon in [exon for exon in exons]:
                    try:
                        if exon.isdigit() and int(exon) <= raw_size:
                            exons[current+'_'+exon] = exons[exon]
                    except:
                        pass
                features.sort(
                    key=lambda feat:(
                        1 if exons[feat['Name']].length == 1 else 0,
                        exons[feat['Name']].start_pos,
                        exons[feat['Name']].end_pos
                    )
                )
                for i in range(len(features)):
                    parts = features[i]['Name'].split('_')
                    prefix = '_'.join(parts[:-1])
                    suffix = parts[-1]
                    if exons[features[i]['Name']].length == 1:
                        features[i][reader.fieldnames[-1]] = 0
                    suffix = str(i)
                    features[i]['Name'] = prefix+'_'+suffix
                writer.writerows(features)
            current = gene
            features = []
        features.append({k:v for k,v in line.items()})
    if len(features):
        ref = gtf.get_gene(current)
        try:
            if len(ref):
                ref = ref[0]
        except:
            pass
        exons = {exon.id:exon for transcript in ref.transcripts for exon in transcript.exons}
        raw_size = len(exons)
        for exon in [exon for exon in exons]:
            try:
                if exon.isdigit() and int(exon) <= raw_size:
                    exons[current+'_'+exon] = exons[exon]
            except:
                pass
        features.sort(
            key=lambda feat:(
                1 if exons[feat['Name']].length == 1 else 0,
                exons[feat['Name']].start_pos,
                exons[feat['Name']].end_pos
            )
        )
        for i in range(len(features)):
            prefix, suffix = features[i]['Name'].split('_')
            if exons[features[i]['Name']].length == 1:
                features[i]['Counts'] = 0
            suffix = str(i)
            features[i]['Name'] = prefix+'_'+suffix
            writer.writerows(features)
    print("Cleaning up")
    w.flush()
    args.gct.close()
    shutil.copyfile(
        args.gct.name,
        args.gct.name+'.bak'
    )
    shutil.copyfile(
        w.name,
        args.gct.name
    )


def main():
    parser = argparse.ArgumentParser('flipper')

    parser.add_argument(
        'gct',
        type=argparse.FileType('r'),
        help="RNA-SeQC 2 Exon reads gct file"
    )

    parser.add_argument(
        'gtf',
        type=argparse.FileType('r'),
        help="Reference GTF for the exons"
    )

    args = parser.parse_args()
    run(args)

if __name__ == '__main__':
    main()
