Example #1
0
def region_page(region_id):
    dbname = session['db_selected']
    db = get_db()
    try:
        region = region_id.split('-')
        cache_key = 't-region-{}'.format(region_id)
        t = cache.get(cache_key)
        print 'Rendering %sregion: %s' % ('' if t is None else 'cached ',
                                          region_id)
        if t is None:
            chrom = region[0]
            start = None
            stop = None
            if len(region) == 3:
                chrom, start, stop = region
                start = int(start)
                stop = int(stop)
            if start is None or stop - start > REGION_LIMIT or stop < start:
                return render_template(
                    'region.html',
                    genes_in_region=None,
                    variants_in_region=None,
                    chrom=chrom,
                    start=start,
                    stop=stop,
                    coverage=None,
                    csq_order=csq_order,
                    dbname=dbname,
                )
            if start == stop:
                start -= 20
                stop += 20
            genes_in_region = lookups.get_genes_in_region(
                db, chrom, start, stop)
            variants_in_region = lookups.get_variants_in_region(
                db, chrom, start, stop)
            xstart = get_xpos(chrom, start)
            xstop = get_xpos(chrom, stop)
            coverage_array = lookups.get_coverage_for_bases(db, xstart, xstop)
            t = render_template(
                'region.html',
                genes_in_region=genes_in_region,
                variants_in_region=variants_in_region,
                chrom=chrom,
                start=start,
                stop=stop,
                coverage=coverage_array,
                csq_order=csq_order,
                dbname=dbname,
            )
            cache.set(cache_key, t)
        return t
    except Exception, e:
        print 'Failed on region:', region_id, ';Error=', traceback.format_exc()
        abort(404)
Example #2
0
def region_page(region_id):
    db = get_db()
    try:
        region = region_id.split('-')
        cache_key = 't-region-{}'.format(region_id)
        t = cache.get(cache_key)
        if t is None:
            chrom = region[0]
            start = None
            stop = None
            if len(region) == 3:
                chrom, start, stop = region
                start = int(start)
                stop = int(stop)
            if start is None or stop - start > REGION_LIMIT or stop < start:
                return render_template(
                    'region.html',
                    genes_in_region=None,
                    variants_in_region=None,
                    chrom=chrom,
                    start=start,
                    stop=stop,
                    coverage=None
                )
            if start == stop:
                start -= 20
                stop += 20
            genes_in_region = lookups.get_genes_in_region(db, chrom, start, stop)
            variants_in_region = lookups.get_variants_in_region(db, chrom, start, stop)
            xstart = get_xpos(chrom, start)
            xstop = get_xpos(chrom, stop)
            coverage_stats_exomes = lookups.get_coverage_for_bases(db, 'exome_coverage', xstart, xstop)
            coverage_stats_genomes = lookups.get_coverage_for_bases(db, 'genome_coverage', xstart, xstop)
            coverage_stats = {
                "exomes": coverage_stats_exomes,
                "genomes": coverage_stats_genomes
            }
            t = render_template(
                'region.html',
                genes_in_region=genes_in_region,
                variants_in_region=variants_in_region,
                chrom=chrom,
                start=start,
                stop=stop,
                coverage=coverage_stats
            )
        print 'Rendering region: %s' % region_id
        return t
    except Exception, e:
        print 'Failed on region:', region_id, ';Error=', traceback.format_exc()
        abort(404)
Example #3
0
def region_page(region_id):
    db = get_db()
    try:
        region = region_id.split('-')
        cache_key = 't-region-{}'.format(region_id)
        t = cache.get(cache_key)
        print 'Rendering %sregion: %s' % ('' if t is None else 'cached ', region_id)
        if t is None:
            chrom = region[0]
            start = None
            stop = None
            if len(region) == 3:
                chrom, start, stop = region
                start = int(start)
                stop = int(stop)
            if start is None or stop - start > REGION_LIMIT or stop < start:
                return render_template(
                    'region.html',
                    genes_in_region=None,
                    variants_in_region=None,
                    chrom=chrom,
                    start=start,
                    stop=stop,
                    coverage=None,
                    csq_order=csq_order,
                )
            if start == stop:
                start -= 20
                stop += 20
            genes_in_region = lookups.get_genes_in_region(db, chrom, start, stop)
            variants_in_region = lookups.get_variants_in_region(db, chrom, start, stop)
            xstart = get_xpos(chrom, start)
            xstop = get_xpos(chrom, stop)
            coverage_array = lookups.get_coverage_for_bases(db, xstart, xstop)
            t = render_template(
                'region.html',
                genes_in_region=genes_in_region,
                variants_in_region=variants_in_region,
                chrom=chrom,
                start=start,
                stop=stop,
                coverage=coverage_array,
                csq_order=csq_order,
            )
            cache.set(cache_key, t)
        return t
    except Exception, e:
        print 'Failed on region:', region_id, ';Error=', traceback.format_exc()
        abort(404)
Example #4
0
def region_page(region_id):
    db = get_db()
    try:
        region = region_id.split("-")
        cache_key = "t-region-{}".format(region_id)
        t = cache.get(cache_key)
        if t is None:
            chrom = region[0]
            start = None
            stop = None
            if len(region) == 3:
                chrom, start, stop = region
                start = int(start)
                stop = int(stop)
            if start is None or stop - start > REGION_LIMIT or stop < start:
                return render_template(
                    "region.html",
                    genes_in_region=None,
                    variants_in_region=None,
                    chrom=chrom,
                    start=start,
                    stop=stop,
                    coverage=None,
                )
            if start == stop:
                start -= 20
                stop += 20
            genes_in_region = lookups.get_genes_in_region(db, chrom, start, stop)
            variants_in_region = lookups.get_variants_in_region(db, chrom, start, stop)
            xstart = get_xpos(chrom, start)
            xstop = get_xpos(chrom, stop)
            coverage_array = lookups.get_coverage_for_bases(db, xstart, xstop)
            t = render_template(
                "region.html",
                genes_in_region=genes_in_region,
                variants_in_region=variants_in_region,
                chrom=chrom,
                start=start,
                stop=stop,
                coverage=coverage_array,
            )
        print "Rendering region: %s" % region_id
        return t
    except Exception, e:
        print "Failed on region:", region_id, ";Error=", e
        abort(404)
Example #5
0
def region_page(region_id):
    db = get_db()
    try:
        region = region_id.split('-')
        cache_key = 't-region-{}'.format(region_id)
        t = cache.get(cache_key)
        if t is None:
            chrom = region[0]
            start = None
            stop = None
            if len(region) == 3:
                chrom, start, stop = region
                start = int(start)
                stop = int(stop)
            if start is None or stop - start > REGION_LIMIT:
                return render_template(
                    'region.html',
                    genes_in_region=None,
                    variants_in_region=None,
                    chrom=chrom,
                    start=start,
                    stop=stop,
                    coverage=None
                )
            genes_in_region = lookups.get_genes_in_region(db, chrom, start, stop)
            variants_in_region = lookups.get_variants_in_region(db, chrom, start, stop)
            xstart = xbrowse.get_xpos(chrom, start)
            xstop = xbrowse.get_xpos(chrom, stop)
            coverage_array = lookups.get_coverage_for_bases(db, xstart, xstop)
            t = render_template(
                'region.html',
                genes_in_region=genes_in_region,
                variants_in_region=variants_in_region,
                chrom=chrom,
                start=start,
                stop=stop,
                coverage=coverage_array
            )
        print 'Rendering region: %s' % region_id
        return t
    except Exception, e:
        print 'Failed on region:', region_id, ';Error=', e
        abort(404)
Example #6
0
def region_page(region_id):
    db = get_db()
    try:
        region = region_id.split('-')
        cache_key = 't-region-{}'.format(region_id)
        t = cache.get(cache_key)
        if t is None:
            chrom = region[0]
            start = None
            stop = None
            if len(region) == 3:
                chrom, start, stop = region
                start = int(start)
                stop = int(stop)
            if start is None or stop - start > REGION_LIMIT:
                return render_template('region.html',
                                       genes_in_region=None,
                                       variants_in_region=None,
                                       chrom=chrom,
                                       start=start,
                                       stop=stop,
                                       coverage=None)
            genes_in_region = lookups.get_genes_in_region(
                db, chrom, start, stop)
            variants_in_region = lookups.get_variants_in_region(
                db, chrom, start, stop)
            xstart = xbrowse.get_xpos(chrom, start)
            xstop = xbrowse.get_xpos(chrom, stop)
            coverage_array = lookups.get_coverage_for_bases(db, xstart, xstop)
            t = render_template('region.html',
                                genes_in_region=genes_in_region,
                                variants_in_region=variants_in_region,
                                chrom=chrom,
                                start=start,
                                stop=stop,
                                coverage=coverage_array)
        print 'Rendering region: %s' % region_id
        return t
    except Exception, e:
        print 'Failed on region:', region_id, ';Error=', e
        abort(404)