def load_exon_sequence(bed, directory, genome_path):
"""Load the exon sequence from the the transcripts.
Input BED format should contain:
blockCount - The number of blocks (exons) in the BED line.
blockSizes - A comma-separated list of the block sizes.
blockStarts - A comma-separated list of block starts.
see details: http://genome.ucsc.edu/FAQ/FAQformat#format1
Output:
Each FASTA file represants a transcript and contains all the exons within the file.
"""
regionset = GenomicRegionSet("bed")
regionset.read(bed)
regionset.sort()
genome = pysam.Fastafile(genome_path)
try:
if len(regionset.sequences[0].data.split("\t")) == 7:
blockinfor = True
no_exon = False
except:
blockinfor = False
regionset.sequences.sort(key=lambda g: g.name)
no_exon = True
if blockinfor:
for gr in regionset:
if not gr.name:
print("Error: For fetching exon sequences, please define the transcript name.")
sys.exit()
else:
if not os.path.exists(directory):
os.makedirs(directory)
f = open(os.path.join(directory, gr.name+".fa"), "w")
data = gr.data.split("\t")
#print(len(data))
if len(data) == 7:
#print(data)
n = int(data[4])
blocks = [ int(b) for b in filter(None, data[5].split(",")) ]
starts = [ int(s) for s in filter(None, data[6].split(",")) ]
printstr = []
for i in range(n):
start = gr.initial + starts[i]
end = start + blocks[i]
if no_exon and i == 0:
ex = ""
elif gr.orientation == "-":
ex = "exon:"+str(n-i)
else:
ex = "exon:"+str(i+1)
if gr.orientation == "-":
seq = Seq(genome.fetch(gr.chrom, start-1, end-1), IUPAC.unambiguous_dna)
seq = seq.reverse_complement()
p = [ ">"+ " ".join([ gr.name,
ex,
"_".join(["REGION",gr.chrom,
str(start),str(end),
gr.orientation]) ]),
seq ]
printstr.append(p)
else:
p = [ ">"+ " ".join([gr.name, ex,
"_".join(["REGION",gr.chrom,str(start),str(end), gr.orientation]) ]),
genome.fetch(gr.chrom, start-1, end-1)
]
printstr.append(p)
if gr.orientation == "-": printstr = printstr[::-1]
for i in range(n):
print(printstr[i][0], file=f)
print(printstr[i][1], file=f)
else:
print("Warning: The given regions have no block information, please try write_bed_blocks")
f.close()
else:
pre_id = ""
for gr in regionset:
if not gr.name:
gr.name = gr.toString()
if pre_id == "":
pre_id = gr.name
z = GenomicRegionSet(gr.name)
z.add(gr)
elif gr.name == pre_id:
z.add(gr)
else:
f = open(os.path.join(directory, pre_id+".fa"), "w")
for i, g in enumerate(z):
try: regiontag = "_".join(["REGION", g.chrom, str(g.initial),str(g.final), gr.orientation])
except: regiontag = "_".join(["REGION", g.chrom, str(g.initial),str(g.final)] )
print( ">"+ " ".join([g.name,
regiontag ]), file=f)
print(genome.fetch(g.chrom, g.initial, g.final), file=f)
f.close()
pre_id = gr.name
z = GenomicRegionSet(gr.name)
z.add(gr)
# Last TX
f = open(os.path.join(directory, pre_id+".fa"), "w")
for i, g in enumerate(z):
try: regiontag = "_".join(["REGION", g.chrom, str(g.initial),str(g.final), gr.orientation])
except: regiontag = "_".join(["REGION", g.chrom, str(g.initial),str(g.final)] )
print( ">"+ " ".join([g.name,
regiontag ]), file=f)
print(genome.fetch(g.chrom, g.initial, g.final), file=f)
f.close()
##################################################################################
parser = argparse.ArgumentParser(
description='Replace TCONs in BED file by assoicated gene names',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-bed',
type=str,
help="BED file or a directory containing BED files")
parser.add_argument('-output', type=str, help="Define the output directory")
parser.add_argument('-organism', type=str, help="Define the organism")
args = parser.parse_args()
genome = GenomeData(args.organism)
if os.path.isfile(args.bed):
regionset = GenomicRegionSet("bed")
regionset.read(args.bed)
gr = regionset.gene_association(organism=args.organism,
promoter_length=1000,
thresh_dist=500000,
show_dis=True)
regionset.replace_region_name(gr, combine=True)
regionset.write(args.output)
elif os.path.isdir(args.bed):
if not os.path.exists(args.output):
os.makedirs(args.output)
for root, dirnames, filenames in os.walk(args.bed):
for filename in filenames:
if ".bed" in filename:
from rgt.ExperimentalMatrix import *
#from fisher import pvalue
import scipy.stats
outdir = ""
back = False
designFile = sys.argv[1]
genomeName = sys.argv[2]
geneFile = sys.argv[3]
randomize = int(sys.argv[4])
backGroundPeaks = False
if len(sys.argv) > 5:
backGroundPeaksName = sys.argv[6]
backBed = GenomicRegionSet("BACK")
backBed.read(backGroundPeaksName)
backGroundPeaks = True
distance = 50000
if len(sys.argv) > 6:
distance = len(sys.argv[6])
if len(sys.argv) > 7:
outdir = sys.argv[7]
#genomeFile=anotationPath+"chrom.sizes"
#geneFile=anotationPath+"association_file.bed"
exps = ExperimentalMatrix()
exps.read(designFile)
#from fisher import pvalue
import scipy.stats
outdir=""
back=False
designFile = sys.argv[1]
genomeName = sys.argv[2]
geneFile = sys.argv[3]
randomize = int(sys.argv[4])
backGroundPeaks=False
if len(sys.argv) > 5:
backGroundPeaksName = sys.argv[6]
backBed=GenomicRegionSet("BACK")
backBed.read(backGroundPeaksName)
backGroundPeaks=True
distance=50000
if len(sys.argv) > 6:
distance=len(sys.argv[6])
if len(sys.argv) > 7:
outdir=sys.argv[7]
#genomeFile=anotationPath+"chrom.sizes"
#geneFile=anotationPath+"association_file.bed"
exps=ExperimentalMatrix()
exps.read(designFile)
##################################################################################
parser = argparse.ArgumentParser(description='Replace TCONs in BED file by assoicated gene names',
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-bed', type=str, help="BED file or a directory containing BED files")
parser.add_argument('-output', type=str, help="Define the output directory")
parser.add_argument('-organism', type=str, help="Define the organism")
args = parser.parse_args()
genome = GenomeData(args.organism)
if os.path.isfile(args.bed):
regionset = GenomicRegionSet("bed")
regionset.read(args.bed)
gr = regionset.gene_association(organism=args.organism, promoter_length=1000,
thresh_dist=500000, show_dis=True)
regionset.replace_region_name(gr,combine=True)
regionset.write(args.output)
elif os.path.isdir(args.bed):
if not os.path.exists(args.output):
os.makedirs(args.output)
for root, dirnames, filenames in os.walk(args.bed):
for filename in filenames:
if ".bed" in filename:
print(filename)
fnn = os.path.basename(filename)