args = parser.parse_args()
entryNumber = args.entryNumber
#
# We assume that the hg19 coordinates and the GRCh37-lite coordinates
# are sorted in the same sort order: by chrom and then chromStart.
# There might be hg19 entries missing from the GRCh37 coordinates,
# as some pieces of hg19 are not in GRCh37-lite. For each line in the
# GRCh37-lite file, read to the corresponding entry in the hg19 file.
# If we read to the end of the hg19 file without finding the
# entry we're looking for, print out a big error message.
hg19Fp = open(args.hg19Bed)
grch37LiteFp = open(args.grch37LiteBed)
for grch37LiteRow in grch37LiteFp:
grch37LiteBed = Bed.Bed(grch37LiteRow.rstrip().split())
for hg19Row in hg19Fp:
hg19Bed = Bed.Bed(hg19Row.rstrip().split())
if hg19Bed.name == grch37LiteBed.name:
break
if hg19Bed.name != grch37LiteBed.name:
sys.exit("Error: missing entry for %s in the GRCh37-lite bed" %
(hg19Bed.name))
gg = Grch37LiteGaf.GafDbSnp(grch37LiteBed, entryNumber=entryNumber)
gg.featureInfo = basicSnpInfo(hg19Bed, args.snpTable, cursor)
(gg.gene, gg.geneLocus) = mapSnpToLocus(grch37LiteBed, gg.featureInfo,
cursor)
entryNumber = entryNumber + 1
gg.entryNumber = entryNumber
gg.write(sys.stdout)
exit(0)
parser = argparse.ArgumentParser()
parser.add_argument(
'inputPsl',
type=str,
help="PSL file from which selected records will be printed")
parser.add_argument('inputBed',
type=str,
help="Bed file to be used for screening the PSL records")
args = parser.parse_args()
bedAlignments = dict()
bedFp = open(args.inputBed)
for line in bedFp:
line = line.rstrip()
bedAlign = Bed.Bed(line.split())
bedAlignments[bedAlign.name] = bedAlign
bedFp.close()
pslFp = open(args.inputPsl)
readPastHeader = False
for line in pslFp:
line = line.rstrip()
if re.search("^--", line):
readPastHeader = True
else:
if readPastHeader:
pslAlign = Psl.Psl(line.split())
if bedAlignments.has_key(pslAlign.qName):
if bedIsSubsetOfPsl(bedAlignments[pslAlign.qName], pslAlign):
print line
idToLabel = dict()
gffIter = GFF.parse(args.inputGff)
for chrom in gffIter:
for hit in chrom.features:
id = hit.id
label = "%s|%s" % (hit.qualifiers["Name"][0], hit.qualifiers["ID"][0])
idToLabel[id] = label
if hit.type == "miRNA":
miRnaToPreMiRna[hit.id] = hit.qualifiers["derives_from"][0]
#
# Read the bed file containing the GRCh37-lite coordinates.
# While converting each line to GAF format, replace the ID
# with the miRNA name, look up the name of the pre-miRNA that
# the miRNA is derived from, and note that in the featureInfo field.
miRnaBedFp = open(args.miRnaBed)
for line in miRnaBedFp:
bb = Bed.Bed(line.rstrip().split())
gg = Grch37LiteGaf.GafMiRna(bb)
gg.featureId = idToLabel[gg.featureId]
preMiRnaId = miRnaToPreMiRna[bb.name]
preMiRnaName = idToLabel[preMiRnaId]
gg.featureInfo = "pre-miRNA=%s" % (preMiRnaName)
(geneName, geneLocus) = preMiRnaGeneLookup(preMiRnaName, cursor)
gg.gene = geneName
gg.geneLocus = geneLocus
entryNumber = entryNumber + 1
gg.entryNumber = entryNumber
gg.write(sys.stdout)
exit(0)
help="Probe BED file, GRCh37-lite coordinates")
parser.add_argument("-n",
dest="entryNumber",
help="Initial entry number",
default=0)
parser.add_argument("-d",
dest="debug",
help="Optional debugging info",
default=False)
args = parser.parse_args()
entryNumber = args.entryNumber
fp = open(args.grch37LiteBed)
for line in fp:
line = line.rstrip()
grch37LiteBed = Bed.Bed(line.split())
gg = Grch37LiteGaf.GafMaProbe(grch37LiteBed, entryNumber)
#
# Look up any overlapping genes. If multiple overlapping genes are found,
# parse the genes and gene locus strings into semicolon-delimited lists.
geneXrefQuery = """SELECT DISTINCT geneName, grch37LiteLocus
FROM gafGeneXref
WHERE grch37LiteChrom = '%s' AND grch37LiteChromStart <= %s
AND grch37LiteChromEnd >= %s
and grch37LiteStrand = '%s'""" % (
grch37LiteBed.chrom, grch37LiteBed.chromEnd, grch37LiteBed.chromStart,
grch37LiteBed.strand)
cursor.execute(geneXrefQuery)
if (args.debug):
print "executing query", geneXrefQuery
parser.add_argument("-n",
dest="entryNumber",
help="Initial entry number",
default=0)
args = parser.parse_args()
db = MySQLdb.connect(host="localhost",
db="hg19",
read_default_file="~/.my.cnf")
cursor = db.cursor(MySQLdb.cursors.DictCursor)
entryNumber = args.entryNumber
fp = open(args.inputBed)
for line in fp:
line = line.rstrip()
bb = Bed.Bed(line.split())
tokens = bb.name.split(";")
clusterId = tokens.pop()
bb.name = ";".join(tokens)
gg = Grch37LiteGaf.GafGene(bb, entryNumber, True)
geneXrefQuery = """SELECT geneName, grch37LiteLocus FROM gafGeneXref
WHERE clusterId = '%s'""" % (clusterId)
cursor.execute(geneXrefQuery)
if cursor.rowcount == 1:
row = cursor.fetchone()
gg.gene = row["geneName"]
gg.featureId = row["geneName"]
gg.geneLocus = row["grch37LiteLocus"]
entryNumber = entryNumber + 1
gg.write(sys.stdout)
exit(entryNumber)
type=str,
help="Input bed file in GRCh37-lite coordinates")
args = parser.parse_args()
db = MySQLdb.connect(host="localhost",
db="hg19",
read_default_file="~/.my.cnf")
cursor = db.cursor(MySQLdb.cursors.DictCursor)
#
# First, make a dictionary of the hg19 coordinates of each gene
hg19Coordinates = dict()
hg19Fp = open(args.hg19Bed)
for line in hg19Fp:
line = line.rstrip()
bb = Bed.Bed(line.split())
hg19Coordinates[bb.name] = bb
hg19Fp.close
#
# Next, read through each entry in GRCh37-lite coordinates.
# At each entry, look up the hg19 coordinates, which will be
# used later for comparison with other tables in hg19. Also at
# each entry, separate the gene name and cluster ID, build a
# GRCh37-lite locus string, and store the gene name, cluster ID,
# gene locus string, and hg19 coordinates within separate columns.
lineCount = 0
grch37LiteFp = open(args.grch37LiteBed)
for line in grch37LiteFp:
line = line.rstrip()
grch37LiteCoords = Bed.Bed(line.split())