def get_feature_data(ref_seq):
"""
:param ref_seq(chromosome): the query string in the format of (refseq_name)?start=234&end=5678
:return: json of the features
JBrowse Track should look like:
{
"label": "my_rest_track",
"key": "REST Test Track",
"type": "JBrowse/View/Track/HTMLFeatures",
"storeClass": "JBrowse/Store/SeqFeature/REST",
"baseUrl": "http://ip_address/JBrowse",
"query": {
"type": "vcf" || "transcript"
"experiment_id": "experiment-id1_experiment-id2" (experiment_id should relate to sample in vcf)
}
}
curl -i http://127.0.0.1:5000/JBrowse/features/chr7?start=123615\&end=208824\&type=vcf\&experiment_id=10_8&vcf_file=
curl -i http://127.0.0.1:5000//jsrv/JBrowse/features/chr1?type=vcf\&experiment_id=70_71\&vcf_file=%2Fdata%2Fscratch%2Fs3_data%2Fpatient-data-results.ctig.com%2FRebiopBarRB3%2FDNA_BWA_CTIG_2013_6_17%2FSTRELKA__VID__115__EIDS__70__72__BIDS__415__419__BCODES__Rebiop-Normal-DNA_ExomeAgilentV5TruSeq-6-19-25-22-70-__Rebiop-TumorPostTx-DNA_ExomeAgilentV5TruSeq-6-20-26-23-72-__all.somatic.indels.dbsnp.snpeff.annotated.gwas.vcf.gz\&start=137499999\&end=149999999
"""
res = {}
res['features'] = []
chr = ref_seq
start= request.args.get('start')
end = request.args.get('end')
type = request.args.get('type')
cur = conn.cursor()
if type == 'vcf':
vcf_file = urllib.unquote_plus(request.args.get('vcf_file'))
experiment_ids = request.args.get('experiment_id').split('_')
# results = query_psql(chr, start, end, experiment_ids, cur)
results = query_multicorn(vcf_file, chr, start, end, cur)
print results
#return json.dumps({'res': len(results)})
return vcf_json(results, cur)
__author__ = 'urvishparikh'
from jbrowse_json_builder import vcf_json
from collections import namedtuple
import psycopg2
vcf_line = namedtuple('vcf_line', ['contig', 'pos', 'ref', 'alt', 'info', 'filter', 'rsid', 'experiment_id', 'ref_cnt', 'alt_cnt'])
conn = psycopg2.connect("dbname=ctig user=urvish")
cur = conn.cursor()
# print vcf_json([vcf_line(contig='(7,1)', pos=123617, ref='A', alt='T', info='NT=ref;QSS=1;QSS_NT=0;SGT=AT->AT;SOMATIC;TQSS=1;TQSS_NT=1', filter='QSS_ref', rsid='', experiment_id=10, ref_cnt=6, alt_cnt=0),
# vcf_line(contig='(7,1)', pos=123617, ref='A', alt='T', info='NT=ref;QSS=1;QSS_NT=0;SGT=AT->AT;SOMATIC;TQSS=1;TQSS_NT=1', filter='QSS_ref', rsid='', experiment_id=8, ref_cnt=0, alt_cnt=2),
# vcf_line(contig='(7,1)', pos=208819, ref='C', alt='A', info='NT=ref;QSS=1;QSS_NT=1;SGT=AC->AC;SOMATIC;TQSS=1;TQSS_NT=1', filter='QSS_ref', rsid='', experiment_id=10, ref_cnt=120, alt_cnt=0),
# vcf_line(contig='(7,1)', pos=208819, ref='C', alt='A', info='NT=ref;QSS=1;QSS_NT=1;SGT=AC->AC;SOMATIC;TQSS=1;TQSS_NT=1', filter='QSS_ref', rsid='', experiment_id=8, ref_cnt=190, alt_cnt=7)],
# cur)
print vcf_json([vcf_line(contig='(1,1)', pos=93586207, ref='G', alt='A',
info='NT=ref;QSS=25;QSS_NT=25;SGT=GG->AG;SOMATIC;TQSS=2;TQSS_NT=2;EFF=STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W198*|491|MTF2||CODING|NM_001164391.1|10|1),STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W198*|491|MTF2||CODING|NM_001164393.1|7|1),STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W300*|536|MTF2||CODING|NM_001164392.1|9|1),STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W300*|593|MTF2||CODING|NM_007358.3|9|1)',
filter='PASS', rsid='', experiment_id=10, ref_cnt=77, alt_cnt=0), vcf_line(contig='(1,1)',
pos=93586207,
ref='G', alt='A',
info='NT=ref;QSS=25;QSS_NT=25;SGT=GG->AG;SOMATIC;TQSS=2;TQSS_NT=2;EFF=STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W198*|491|MTF2||CODING|NM_001164391.1|10|1),STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W198*|491|MTF2||CODING|NM_001164393.1|7|1),STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W300*|536|MTF2||CODING|NM_001164392.1|9|1),STOP_GAINED(HIGH|NONSENSE|tGg/tAg|W300*|593|MTF2||CODING|NM_007358.3|9|1)',
filter='PASS', rsid='',
experiment_id=8, ref_cnt=207,
alt_cnt=6)], cur)