def main():
parser = argparse.ArgumentParser()
parser.add_argument('input', help="GENEPRED file input use - for STDIN")
args = parser.parse_args()
inf = sys.stdin
if args.input != '-':
inf = open(args.input)
for line in inf:
e = GenePredBasics.GenePredEntry()
e.line_to_entry(line.rstrip())
print e.entry['gene_name'] + "\t" + e.entry['name'] + "\t" + str(
e.length())
inf.close()
def add_genepred_line(self, inline):
if not self.ref_hash:
sys.stderr.write(
"ERROR: Must assign a reference genome dictionary first\n")
sys.exit()
gpd = GenePredBasics.GenePredEntry(inline)
if gpd.value('name') in self.transcripts:
sys.stderr.write("WARNING: " + inline +
" transcript was already set\n")
seq = ''
for i in range(0, gpd.value('exonCount')):
seq += self.ref_hash[gpd.value('chrom')][
gpd.value('exonStarts')[i]:gpd.value('exonEnds')[i]].upper()
if gpd.value('strand') == '-': seq = SequenceBasics.rc(seq)
self.transcripts[gpd.value('name')] = seq
return
def main():
parser = argparse.ArgumentParser(description='Create artifical reference sequences from a genepred')
parser.add_argument('gpd_file')
parser.add_argument('reference_fasta')
parser.add_argument('-o','--output',help="output file to write to or STDOUT if not set")
args = parser.parse_args()
of = sys.stdout
if args.output: of = open(args.output,'w')
f = read_fasta_into_hash(args.reference_fasta)
with open(args.gpd_file) as inf:
for line in inf:
gpd = GenePredBasics.GenePredEntry()
gpd.line_to_entry(line.rstrip())
ars = ARS()
beds = []
for i in range(0,gpd.value('exonCount')):
b = Bed(gpd.value('chrom'),gpd.value('exonStarts')[i],gpd.value('exonEnds')[i],gpd.value('strand'))
beds.append(b)
ars.set_bounds(beds)
ars.set_name(gpd.value('name'))
ars.set_sequence_from_original_reference_hash(f)
of.write(ars.get_fasta())
def main():
parser = argparse.ArgumentParser(
description=
"Make a universal genepred and key for comparing IDP results")
parser.add_argument(
'--output_directory',
default='IDP_output_merge',
help='DIRECTORY to write output to. Will not overwrite existing')
parser.add_argument(
'genepred_exp_name_sets',
nargs='+',
help=
"three files for each IDP entry 1) a genepred 2) an expression file 3) a sample name."
)
args = parser.parse_args()
mydir = args.output_directory.rstrip('/')
if os.path.isdir(mydir):
sys.stderr.write("ERROR: output directory " + mydir +
" already exists\n")
return
os.makedirs(mydir)
set_args = args.genepred_exp_name_sets
if len(set_args) % 3 != 0:
sys.stderr.write("Data must be in sets of three")
setnum = 0
resultnumber = 0
numbers = {}
byset = {}
chromosomes = set()
established_names = {}
expression = {}
sample_names = set()
while len(set_args) > 0:
setnum += 1
gpd = set_args.pop(0)
exp = set_args.pop(0)
sample_name = set_args.pop(0)
sample_names.add(sample_name)
sys.stderr.write("Set: " + str(setnum) + "\n")
sys.stderr.write(" GenePred: " + gpd + "\n")
sys.stderr.write(" Expression: " + exp + "\n")
sys.stderr.write(" Sample: " + sample_name + "\n")
with open(gpd) as inf:
for line in inf:
if re.match('^#', line): continue
e = GenePredBasics.GenePredEntry()
e.line_to_entry(line)
chromosomes.add(e.entry['chrom'])
junctions = e.junctions
resultnumber += 1
junstring = ";".join(junctions)
if junstring not in byset:
byset[junstring] = set()
byset[junstring].add(resultnumber)
numbers[resultnumber] = [sample_name, e.entry['name'], e]
with open(exp) as inf:
for line in inf:
f = line.rstrip().split("\t")
if sample_name not in expression:
expression[sample_name] = {}
expression[sample_name][f[0]] = [float(
f[1]), float(f[2])] #transcript and gene exression
#bysample = {}
gene_records = {}
for junc in byset:
lowest = False
highest = False
realnames = set()
realgenenames = set()
chromnames = set()
chromgenenames = set()
arbitrary_gpd = False
sgpds = {}
for i in byset[junc]:
[sample, name, gpd] = numbers[i]
gene_name = gpd.entry['gene_name']
arbitrary_gpd = gpd
sgpds[sample] = gpd
# Figure out if its a reference transcript name or an IDP manufactured name
m = re.match('^([^:]+):\d+-\d+', name)
if not m:
realnames.add(name)
else:
chromnames.add(m.group(1))
# Figure out if its a reference gene name or an IPD manufacture gene anme
m = re.match('^([^:]+):\d+-\d+', gene_name)
if not m:
realgenenames.add(gene_name)
else:
chromgenenames.add(m.group(1))
if not lowest or gpd.entry['txStart'] < lowest:
lowest = gpd.entry['txStart']
if not highest or gpd.entry['txEnd'] > highest:
highest = gpd.entry['txEnd']
#if sample not in bysample:
# bysample[sample] = {}
#if name not in bysample[sample]:
# bysample[sample][name] = i
usename = False
basename = False
if len(realnames) > 0:
usename = next(iter(realnames))
if len(realnames) > 1:
sys.stderr.write(
"WARNING: multiple transcript names as with the same junctions.\n"
+ str(realnames) + "\nUsing: " + str(usename) + "\n")
if usename in established_names:
sys.stderr.write(
"WARNING: reference transcript name " + usename +
" refers to different transcripts with different junction compositions. Renaming the second instance to a unique name."
)
established_names[usename] += 1
usename = usename + '.' + str(established_names[usename])
else:
established_names[usename] = 0
else:
usechrom = next(iter(chromnames))
if len(chromnames) > 1:
sys.stderr.write(
"ERROR: multiple chromosome names are not supported in a single transcript yet.\n"
+ str(chromnames) + "\n")
sys.exit()
basename = usechrom + ":" + str(lowest) + '-' + str(highest)
if basename not in established_names:
established_names[basename] = 0
established_names[basename] += 1
usename = basename + '.' + str(established_names[basename])
# See if we have a real gene name for base name
if len(realgenenames) > 0:
basename = next(iter(realgenenames))
#print basename + "\t" + usename
if basename not in gene_records:
gene_records[basename] = {}
gene_records[basename][usename] = {}
gene_records[basename][usename]['sample_gpd'] = {}
gene_records[basename][usename]['sample_exp'] = {}
gene_records[basename][usename]['gpd'] = GenePredBasics.GenePredEntry()
# copy the old record
gene_records[basename][usename]['gpd'].line_to_entry(
arbitrary_gpd.get_line())
if lowest < gene_records[basename][usename]['gpd'].entry['txStart']:
sys.stderr.write("ADJUSTING NEW GPD TXSTART FOR " + basename +
" " + usename + "\n")
gene_records[basename][usename]['gpd'].entry['txStart'] = lowest
gene_records[basename][usename]['gpd'].entry['cdsStart'] = lowest
gene_records[basename][usename]['gpd'].entry['exonStarts'][
0] = lowest
if highest > gene_records[basename][usename]['gpd'].entry['txEnd']:
sys.stderr.write("ADJUSTING NEW GPD TXEND FOR " + basename + " " +
usename + "\n")
gene_records[basename][usename]['gpd'].entry['txEnd'] = highest
gene_records[basename][usename]['gpd'].entry['cdsEnd'] = highest
gene_records[basename][usename]['gpd'].entry['exonEnds'][
len(gene_records[basename][usename]['gpd'].entry['exonEnds']) -
1] = lowest
# Now add the original sample information
for sample in sgpds:
gene_records[basename][usename]['sample_gpd'][sample] = sgpds[
sample]
gene_records[basename][usename]['sample_exp'][sample] = expression[
sample][sgpds[sample].entry['name']][0]
#Now all necessary data should be in gene_records
sample_list = sorted(list(sample_names))
ofgene = open(mydir + '/gene.exp', 'w')
ofgene.write("gene")
for sample in sample_list:
ofgene.write("\t" + sample)
ofgene.write("\n")
geneexp = {}
for gene in gene_records:
total = {}
for sample in sample_list:
total[sample] = 0
geneexp[gene] = {}
for transcript in gene_records[gene]:
for sample in gene_records[gene][transcript]['sample_exp']:
total[sample] += gene_records[gene][transcript]['sample_exp'][
sample]
ofgene.write(gene)
for sample in sample_list:
geneexp[gene][sample] = total[sample]
ofgene.write("\t" + str(total[sample]))
ofgene.write("\n")
ofgene.close()
#Now we can do all the transcript writing
ofgeneiso = open(mydir + '/gene_isoform.exp', 'w')
ofgeneiso.write("gene\tisoform")
for sample in sample_list:
ofgeneiso.write("\t" + sample + ".gene" + "\t" + sample + ".isoform")
ofgeneiso.write("\n")
ofiso = open(mydir + '/isoform.exp', 'w')
ofiso.write("isoform")
for sample in sample_list:
ofiso.write("\t" + sample)
ofiso.write("\n")
for gene in gene_records:
for transcript in gene_records[gene]:
ofiso.write(transcript)
ofgeneiso.write(gene + "\t" + transcript)
for sample in sample_list:
if sample in gene_records[gene][transcript]['sample_exp']:
ofgeneiso.write("\t" + str(geneexp[gene][sample]) + "\t" +
str(gene_records[gene][transcript]
['sample_exp'][sample]))
ofiso.write("\t" + str(gene_records[gene][transcript]
['sample_exp'][sample]))
else:
ofiso.write("\t0")
if sample in geneexp[gene]:
ofgeneiso.write("\t" + str(geneexp[gene][sample]) +
"\t0")
else:
ofgeneiso.write("0\t0")
ofiso.write("\n")
ofgeneiso.write("\n")
ofiso.close()
#Maybe we can finish it all off by writing the new genepred
ofgpd = open(mydir + '/isoform.gpd', 'w')
for gene in gene_records:
for transcript in gene_records[gene]:
ofgpd.write(gene_records[gene][transcript]['gpd'].get_line() +
"\n")
ofgpd.close()
