def main(options):
included_assaytypes = {
"affy": 1,
"illumina": 1,
"broad": 1,
"metabo": 1,
"exome": 1
}
godb = GoDb()
# Data structures
atype_list = []
atype_posns = {}
marker_list = []
rsid_assaytypes = {}
rsid_dict = {}
rsid_prfx_dict = {}
rsid_cr_dict = {}
rsid_info_dict = {}
count = 0
# Step 1 - get the list of entries for each rsid - one per assaytype
vardocs = godb.get_multiple_variants(options.rsid)
sampposns = godb.get_sample_posns(options.sampleid)
for doc in vardocs:
filepath = godb.get_filepath(doc["assaytype"], doc["chromosome"])
rec = godb.get_variant_file_data(filepath, doc["chromosome"],
doc["position"])
vcfr = VCFrecord(rec)
prfx, sfx = vcfr.get_prfx_sfx()
if doc["assaytype"] in sampposns:
print "%s,%s,%s,%d,%s" % (
options.rsid, options.sampleid, doc["assaytype"],
sampposns[doc["assaytype"]], sfx[sampposns[doc["assaytype"]]])
return count
def main(options):
#included_assaytypes = {"biggertest":1, "bigtest":1, "affy":1, "illumina":1, "broad":1, "metabo":1, "exome":1}
#included_assaytypes = {"bigtest":1, "affy":1, "illumina":1, "broad":1, "metabo":1, "exome":1}
#included_assaytypes = {"affy":1, "illumina":1, "broad":1, "metabo":1, "exome":1}
#included_assaytypes = {"affy":1, "illumina":1, "broad":1, "exome":1}
#included_assaytypes = {"affy":1, "illumina":1, "broad":1}
#included_assaytypes = {"affy":1, "illumina":1}
included_assaytypes = {"broad":1}
#included_assaytypes = {"metabo":1}
#included_assaytypes = {"affy":1}
#included_assaytypes = {"bigtest":1}
#included_assaytypes = {"biggertest":1}
rsids = []
godb = GoDb()
try:
if options.snpfile != None:
fh = open(options.snpfile, "r")
rsids = load_snpfile_data(fh)
else:
rsids = options.rsids.split(",")
except IOError as e:
print "I/O error({0}): {1}".format(e.errno, e.strerror)
exit()
except TypeError as e:
print "Missing arguments ", e
exit()
except:
logging.info("Unexpected error: %s", str(sys.exc_info()))
sys.exit()
# Step 0 - initialise db connection and instanciate helper objects
mafh = Mafhelper()
hweh = Hwehelper()
# Data structures
atype_list = []
atype_posns = {}
marker_list = []
rsid_assaytypes = {}
rsid_dict = {}
rsid_prfx_dict = {}
rsid_cr_dict = {}
rsid_info_dict = {}
hdr_pref = ["#CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO", "FORMAT"]
# Step 1 - get the list of entries for each rsid - one per assaytype
for rsid in rsids:
#logging.info("Processing rsid = %s", rsid)
docs = godb.get_multiple_variants(rsid)
if docs.count() > 0:
rsid_assaytypes[rsid] = []
else:
logging.info("RSID %s NOTFOUND", rsid)
#print docs
# Step 1a - collect assaytypes and marker documents
# At this point we're establishing a list order which must be observed throughout.
for doc in docs:
#logging.info("%s", str(doc))
if doc["assaytype"] not in included_assaytypes:
continue
if doc["assaytype"] not in atype_list:
atype_list.append(doc["assaytype"])
rsid_assaytypes[rsid].append(doc)
logging.info(str(atype_list))
# Step 2 - collect lists of prochis (sample ids) by assaytype
prochi_list = [[]] * len(atype_list)
for i, atype in enumerate(atype_list):
atype_posns[atype] = i
prochi_list[i] = godb.get_samples(atype)
#logging.info("SAMP %d, %s, %s", i, atype, str(prochi_list[i]))
mm = Multibuffermerge(prochi_list)
# Step 3 - get combined col_header positions
# combo is a dict {posn:colname}
combo = mm.get_combined_positions()
#print len(combo)
# combocol is a list [colname1, colname2, ..., colname] again we keep the order of this intact
combocol = mm.get_combined_columns()
# Step 4 - for each variant by rsid
for rsid in rsid_assaytypes:
if rsid not in rsid_dict:
rsid_prfx_dict[rsid] = [[]] * len(atype_list)
rsid_dict[rsid] = [[]] * len(atype_list)
rsid_cr_dict[rsid] = [[]] * len(atype_list)
rsid_info_dict[rsid] = [[]] * len(atype_list)
#print len(rsid_assaytypes[rsid])
for doc in rsid_assaytypes[rsid]:
if options.prfx != None:
fpath = godb.get_full_filepath(doc["assaytype"], doc["chromosome"], options.prfx)
else:
fpath = godb.get_filepath(doc["assaytype"], doc["chromosome"])
logging.info("Assaytype=%s fpath=%s", doc["assaytype"], fpath)
result = godb.get_variant_file_data(fpath, doc["chromosome"], doc["position"])
if result != None:
vcfr = VCFrecord(result)
varid = vcfr.get_varid()
if varid == rsid:
rec = result
maf, ma, cr = mafh.get_maf_and_cr(vcfr)
# TODO - ALSO check maf, also apply QC filter at individual record level
rsid_cr_dict[doc["rsid"]][atype_posns[doc["assaytype"]]] = cr
rsid_dict[doc["rsid"]][atype_posns[doc["assaytype"]]] = rec
logging.info("%s (%s), maf=%s, ma=%s, cr=%s" % (doc["rsid"], doc["assaytype"], maf, ma, cr))
#print combocol
# Step 5 - execute the merge process
print "\t".join(hdr_pref + combocol)
count = 0
concordant = True
for rsid in rsid_dict:
if len(rsid_dict[rsid][0]) > 0:
if options.check == 'Y':
concordant = mm.check_concordancies(rsid_dict[rsid], atype_list, options.chipval)
if concordant == True:
comborec = mm.get_combined_array(rsid_dict[rsid], rsid_cr_dict[rsid], atype_list)
vcfr = VCFrecord(rsid_dict[rsid][0])
prfx,sfx = vcfr.get_prfx_sfx()
if len(prfx) > 0:
logging.info("PRFX = %s, for %s", str(prfx), rsid)
prfx[8] += ":AT"
outrec = prfx + comborec
print "\t".join(outrec)
count += 1
else:
logging.info("RSID %s NOTFOUND (2)", rsid)
pass
else:
logging.info("Concordancy check fail for - %s" % (rsid))
#chi_test_count, allele_disc_count, overlap_count, cr_check_count = mm.get_counts()
#logging.info("Overlap check count = %d, cr_check_count = %d", overlap_count, cr_check_count)
chi_test_count, allele_disc_count, overlap_count = mm.get_counts()
logging.info("CHI test count = %d, Allele discord count = %d, Overlap check count = %d",
chi_test_count, allele_disc_count, overlap_count)
return count