def run(self):
f = self.begin_output()
for filename in self.filenames:
any = False
name = os.path.splitext(os.path.split(filename)[1])[0]
try:
iterator = io.read_sequences(filename, qualities=True)
except grace.Error:
iterator = None
if iterator is not None:
total = 0
total_length = 0
for seq in io.read_sequences(filename, qualities=True):
total += 1
total_length += len(seq[1])
print >> f, grace.datum(name, 'sequences', total)
print >> f, grace.datum(name, 'average length',
float(total_length) / total)
print >> f
any = True
try:
iterator = annotation.read_annotations(filename)
except grace.Error:
iterator = None
if iterator:
total = 0
counts = {}
for item in iterator:
total += 1
counts[item.type] = counts.get(item.type, 0) + 1
print >> f, grace.datum(name, 'features', total)
for key in sorted(counts):
print >> f, grace.datum(name, key + ' features',
counts[key])
print >> f
any = True
if not any:
raise grace.Error(
filename +
' is neither a sequence file nor an annotation file that nesoni can read.'
)
self.end_output(f)
def run(self):
f = self.begin_output()
for filename in self.filenames:
any = False
name = os.path.splitext(os.path.split(filename)[1])[0]
try:
iterator = io.read_sequences(filename, qualities=True)
except grace.Error:
iterator = None
if iterator is not None:
total = 0
total_length = 0
for seq in io.read_sequences(filename, qualities=True):
total += 1
total_length += len(seq[1])
print >> f, grace.datum(name, 'sequences', total)
print >> f, grace.datum(name, 'average length', float(total_length)/total)
print >> f
any = True
try:
iterator = annotation.read_annotations(filename)
except grace.Error:
iterator = None
if iterator:
total = 0
counts = { }
for item in iterator:
total += 1
counts[item.type] = counts.get(item.type,0)+1
print >> f, grace.datum(name, 'features', total)
for key in sorted(counts):
print >> f, grace.datum(name, key + ' features', counts[key])
print >> f
any = True
if not any:
raise grace.Error(filename + ' is neither a sequence file nor an annotation file that nesoni can read.')
self.end_output(f)
def run(self):
f = self.begin_output()
for filename in self.filenames:
info = io.get_file_info(filename)
any = False
name = os.path.splitext(os.path.split(filename)[1])[0]
if info.matches('sequences'):
total = 0
total_length = 0
for seq in io.read_sequences(filename, qualities=True):
total += 1
total_length += len(seq[1])
print >> f, grace.datum(name, 'sequences', total)
print >> f, grace.datum(name, 'total bases', total_length)
if total:
print >> f, grace.datum(name, 'average length',
float(total_length) / total)
print >> f
any = True
if info.matches('annotations'):
total = 0
counts = {}
for item in annotation.read_annotations(filename, "/"):
total += 1
counts[item.type] = counts.get(item.type, 0) + 1
print >> f, grace.datum(name, 'features', total)
for key in sorted(counts):
print >> f, grace.datum(name, key + ' features',
counts[key])
print >> f
any = True
if info.matches('type-vcf'):
reader_f = io.open_possibly_compressed_file(filename)
reader = vcf.Reader(reader_f)
n = 0
for item in reader:
n += 1
print >> f, grace.datum(name, 'variants', n)
any = True
if not any:
raise grace.Error('Don\'t know what to do with ' + filename)
self.end_output(f)
def run(self):
f = self.begin_output()
for filename in self.filenames:
info = io.get_file_info(filename)
any = False
name = os.path.splitext(os.path.split(filename)[1])[0]
if info.matches('sequences'):
total = 0
total_length = 0
for seq in io.read_sequences(filename, qualities=True):
total += 1
total_length += len(seq[1])
print >> f, grace.datum(name, 'sequences', total)
print >> f, grace.datum(name, 'total bases', total_length)
if total:
print >> f, grace.datum(name, 'average length', float(total_length)/total)
print >> f
any = True
if info.matches('annotations'):
total = 0
counts = { }
for item in annotation.read_annotations(filename):
total += 1
counts[item.type] = counts.get(item.type,0)+1
print >> f, grace.datum(name, 'features', total)
for key in sorted(counts):
print >> f, grace.datum(name, key + ' features', counts[key])
print >> f
any = True
if info.matches('type-vcf'):
reader_f = io.open_possibly_compressed_file(filename)
reader = vcf.Reader(reader_f)
n = 0
for item in reader:
n += 1
print >> f, grace.datum(name, 'variants', n)
any = True
if not any:
raise grace.Error('Don\'t know what to do with ' + filename)
self.end_output(f)
