sys.exit(p.print_help())
args = p.parse_args()
return args
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__=="__main__":
# Get parameters
args=argParser()
fh = IO.mopen(args.ofname, 'w')
lastbed = Bed("chr1\t0\t0")
cnt = 0 # count of unique items
for item in IO.BioReader(args.ifname,args.ftype):
if item.chrom == lastbed.chrom and item.start == lastbed.start and item.stop == lastbed.stop:
if args.names == 'c':
lastbed.id += ";"+item.id
else:
if lastbed.stop !=0:
cnt += 1
if args.names == 'n':
lastbed.id = str(cnt)
elif args.names == 'p':
lastbed.id = args.prefix+"_"+str(cnt)
print >> fh, lastbed
required=False,
help='Output file name. Default is "stdout".')
if len(sys.argv) == 1:
sys.exit(p.print_help())
args = p.parse_args()
return args
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__ == "__main__":
args = argParser()
fh = IO.mopen(args.ofname, 'w')
# Fasta file
fa = FastaFile(args.ifname)
f = IO.mopen(args.names)
for faid in f:
faid = faid.rstrip()
seq = fa.getSeq(faid)
print >> fh, ">" + faid
print >> fh, seq.formatSeq()
fa.close()
IO.mclose(f)
IO.mclose(fh)
args = p.parse_args()
return args
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__ == "__main__":
# Get parameters
args = argParser()
fh = IO.mopen(args.ofname, 'w')
lastbed = Bed("chr1\t0\t0")
cnt = 0 # count of unique items
for item in IO.BioReader(args.ifname, args.ftype):
if item.chrom == lastbed.chrom and item.start == lastbed.start and item.stop == lastbed.stop:
if args.names == 'c':
lastbed.id += ";" + item.id
else:
if lastbed.stop != 0:
cnt += 1
if args.names == 'n':
lastbed.id = str(cnt)
elif args.names == 'p':
lastbed.id = args.prefix + "_" + str(cnt)
print >> fh, lastbed
sys.exit(p.print_help())
args = p.parse_args()
return args
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__ == "__main__":
# Get parameters
args = argParser()
fh = IO.mopen(args.ofname, 'w')
tlen = 0
gccnt = 0
# Read fasta file
for tseq in IO.BioReader(args.fname, 'fasta'):
seq = str(tseq.seq).upper()
cnt = seq.count("G") + seq.count("C")
length = len(seq) - seq.count("N")
print >> fh, "%s\t%-3.3f" % (tseq.id, float(cnt) /
(length and length or 1))
gccnt += cnt
tlen += length
print >> fh, "Total\t%-3.3f" % (float(gccnt) / (tlen and tlen or 1))
IO.mclose(fh)
import sys
import string
from ngslib import IO
# ------------------------------------
# constants
# ------------------------------------
# ------------------------------------
# Misc functions
# ------------------------------------
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__=="__main__":
if len(sys.argv)==1:
sys.exit("Example:"+sys.argv[0]+" anno.tab/bed\n\tPrint TSS position in Bed format.")
if sys.argv[1].endswith(".tab"):
for item in IO.BioReader(sys.argv[1],ftype= 'genepred'):
print item.toBed().getTSS()
else:
for item in IO.BioReader(sys.argv[1],ftype= 'bed'):
print item.getTSS()
if '.tab' in sys.argv[1]:
ftype='gene'
else:
ftype='bed'
# initiation annotations.
annos={}
#for chrom in IO.genomeSize('hg19'):
for chrom in Utils.genomeSize(sys.argv[2]):
if ftype=='bed':
annos[chrom]=BedList()
else:
annos[chrom]=GeneBedList()
# read annotations.
for anno in IO.BioReader(sys.argv[1],ftype=ftype):
if annos.has_key(anno.chrom):
annos[anno.chrom].append(anno)
# sort
for chrom in annos:
annos[chrom].sort()
# Find nearest annoations
for item in IO.BioReader(sys.argv[3],ftype='bed'):
if annos.has_key(item.chrom) and len(annos[item.chrom])>0:
tanno=annos[item.chrom][annos[item.chrom].bisect(item)]
olen=item.overlapLength(tanno)
if olen==1:
annostr=tanno.id+':overlap'
olen=0
# ------------------------------------
# Misc functions
# ------------------------------------
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__ == "__main__":
# Get parameters
args = argParser()
fh = IO.mopen(args.ofname, 'w')
genome = FastaFile(args.genome)
for i, item in enumerate(IO.BioReader(args.ifname, args.ftype)):
try:
strand = item.strand
except:
strand = "+"
seq = item.getSeq(genome)
if len(seq) > 0:
print >> fh, '>' + (item.id != "NONAME" and item.id
or "item_" + str(i))
if args.linelength:
seq = seq.formatSeq(args.linelength)
if args.case == 'u':
seq = seq.upper()
elif args.case == 'l':
if len(sys.argv)==1:
sys.exit(p.print_help())
args = p.parse_args()
return args
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__=="__main__":
args = argParser()
fh = IO.mopen(args.ofname, 'w')
# Parse chromosome region
if args.region:
m = re.search("(\S+):(\S*)-(\S*):(\S*)",args.region)
chrom, start, end, strand = m.groups()
else:
chrom = args.chrom
start = args.start
end = args.end
strand= args.strand
if not chrom:
raise ValueError("chromosome name is required.")
start = int(start) if start else None
end = int(end) if end else None
strand = strand if strand in ["+","-","."] else "+"
# Get seq from Fasta file
# ------------------------------------
# python modules
# ------------------------------------
import sys
import string
from ngslib import IO
# ------------------------------------
# constants
# ------------------------------------
# ------------------------------------
# Misc functions
# ------------------------------------
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__ == "__main__":
if len(sys.argv) == 1:
sys.exit("Example:" + sys.argv[0] + " *.tab ")
for item in IO.BioReader(sys.argv[1], 'genepred'):
for exon in item.exons():
print exon
p.add_argument("-n","--names",dest='names',type=str,metavar="names.lst",required=True,help='A file with sequence names. Can be "stdin".')
p.add_argument("-o","--output",dest='ofname',type=str, default="stdout", metavar="output.fa",required=False,help='Output file name. Default is "stdout".')
if len(sys.argv)==1:
sys.exit(p.print_help())
args = p.parse_args()
return args
# ------------------------------------
# Classes
# ------------------------------------
# ------------------------------------
# Main
# ------------------------------------
if __name__=="__main__":
args = argParser()
fh = IO.mopen(args.ofname, 'w')
# Fasta file
fa = FastaFile(args.ifname)
f = IO.mopen(args.names)
for faid in f:
faid=faid.rstrip()
seq=fa.getSeq(faid)
print >> fh, ">"+faid
print >> fh, seq.formatSeq()
fa.close()
IO.mclose(f)
IO.mclose(fh)