def parse_refgpd(tdir,geneprednames,simplenames):
# get the reference genepreds ready to use in work
column_number = 0
entry_number = 0
of_entries = open(tdir+"/entries.txt",'w')
for file in geneprednames:
column_number += 1
of_ref = open(tdir+"/reference."+str(column_number)+".bed",'w')
gfr = FileBasics.GenericFileReader(file)
while True:
line = gfr.readline()
if not line: break
if re.match('^#',line): continue
entry_number += 1
line = line.rstrip("\n")
entry = GenePredBasics.line_to_entry(line)
entry_length = 0
for i in range(0,len(entry['exonStarts'])): entry_length += entry['exonEnds'][i]-entry['exonStarts'][i]
of_entries.write(str(column_number)+ "\t" + simplenames[column_number-1] + "\t" + str(entry_number) + "\t" + entry['gene_name'] + "\t" + entry['name']+"\t"+str(entry_length)+"\n")
exon_number = 0
for i in range(0,len(entry['exonStarts'])):
exon_number += 1
of_ref.write(entry['chrom'] + "\t" + str(entry['exonStarts'][i]) + "\t" \
+ str(entry['exonEnds'][i]) + "\t" + str(entry_number) + "\t" \
+ entry['gene_name'] + "\t" \
+ entry['name'] + "\t" + str(len(entry['exonStarts'])) + "\t" \
+ entry['strand'] + "\t" + str(exon_number) \
+ "\n")
gfr.close()
of_ref.close()
of_entries.close()
def parse_gpdfile(tdir,gpdfile,smoothing_factor):
# Go through the long reads and make a genepred
if gpdfile != '-':
fr = FileBasics.GenericFileReader(gpdfile)
else:
fr = sys.stdin
seennames = {}
longreadnumber = 0
of_gpd = open(tdir+'/longreads.gpd','w')
while True:
line = fr.readline()
if not line: break
if re.match('^#',line): #skip comments
continue
longreadnumber += 1
entry = GenePredBasics.smooth_gaps( \
GenePredBasics.line_to_entry(line.rstrip()) \
,smoothing_factor)
readname = entry['name']
if readname in seennames:
sys.stderr.write("Warning: repeat name '"+readname+"'\n")
#set our first name to our bin
entry['name'] = str(longreadnumber)
gline = GenePredBasics.entry_to_line(entry)
of_gpd.write(gline+"\n")
fr.close()
of_gpd.close()
def read_fastq_file(self,filename):
gfr = FileBasics.GenericFileReader(filename)
linecount = 0
while True and linecount < self.max_read_count:
line1 = gfr.readline().rstrip()
if not line1: break
line2 = gfr.readline().rstrip()
if not line2: break
line3 = gfr.readline().rstrip()
if not line3: break
line4 = gfr.readline().rstrip()
if not line4: break
self.record_observation(line4)
linecount += 1
gfr.close()