def count_reads_in_features(sam_filename, gff_filename, samtype, order,
stranded, overlap_mode, feature_type, id_attribute,
quiet, minaqual, samout, directory):
forward = stranded in ["yes", "both"]
reverse = stranded in ["reverse", "both"]
is_stranded = stranded != "NO"
if samout != "" and stranded == "both":
raise Exception("Output SAM alignment records not supported "
"for stranded 'both'")
if samtype == "bam":
extensions = [".bam"]
elif samtype == "sam":
extensions = [".sam", ".sam.gz"]
else:
extensions = [".bam", ".sam", ".sam.gz"]
files = brenninc_utils.find_files(sam_filename,
extensions=extensions,
recursive=True)
features, counts = get_features(gff_filename, is_stranded, feature_type,
id_attribute, quiet)
for a_file in files:
if samout == "auto":
samout_file = brenninc_utils.create_new_file(sam_filename,
"_annotated",
outputdir=directory,
extension="sam",
gzipped=False)
else:
samout_file = samout
print "counting", a_file
count_reads(a_file, features, counts, samtype, order, forward, reverse,
overlap_mode, quiet, minaqual, samout_file, directory)
def count_reads_in_features(sam_filename, gff_filename, samtype, order,
stranded, overlap_mode, feature_type,
id_attribute, quiet, minaqual, samout, directory):
forward = stranded in ["yes", "both"]
reverse = stranded in ["reverse", "both"]
is_stranded = stranded != "NO"
if samout != "" and stranded == "both":
raise Exception("Output SAM alignment records not supported "
"for stranded 'both'")
if samtype == "bam":
extensions = [".bam"]
elif samtype == "sam":
extensions = [".sam", ".sam.gz"]
else:
extensions = [".bam", ".sam", ".sam.gz"]
files = brenninc_utils.find_files(sam_filename, extensions=extensions,
recursive=True)
features, counts = get_features(gff_filename, is_stranded, feature_type,
id_attribute, quiet)
for a_file in files:
if samout == "auto":
samout_file = brenninc_utils.create_new_file(sam_filename,
"_annotated",
outputdir=directory,
extension="sam",
gzipped=False)
else:
samout_file = samout
print "counting", a_file
count_reads(a_file, features, counts, samtype, order, forward, reverse,
overlap_mode, quiet, minaqual, samout_file, directory)
def makehead(path,
sequences=100,
outputdir=None,
qual_scale=_default_qual_scale):
files = brenninc_utils.find_files(path, ["fastq", "fastq.gz"])
for afile in files:
head(path=afile,
sequences=sequences,
outputdir=outputdir,
qual_scale=qual_scale)
def count_reads_in_features(sam_filename, gff_filename, samtype, order,
stranded, overlap_mode, feature_type,
id_attribute, quiet, minaqual, samout, directory):
if samtype == "bam":
extensions = [".bam"]
elif samtype == "sam":
extensions = [".sam", ".sam.gz"]
else:
extensions = [".bam", ".sam", ".sam.gz"]
files = brenninc_utils.find_files(sam_filename, extensions=extensions,
recursive=True)
(features, counts) = get_features(gff_filename, stranded, feature_type,
id_attribute, quiet)
for a_file in files:
print "counting", a_file
count_reads_using_features(a_file, features, counts, samtype, order,
stranded, overlap_mode, quiet, minaqual,
samout, directory)
def count_reads_in_features(sam_filename, gff_filename, samtype, order,
stranded, overlap_mode, feature_type, id_attribute,
quiet, minaqual, samout, directory):
if samtype == "bam":
extensions = [".bam"]
elif samtype == "sam":
extensions = [".sam", ".sam.gz"]
else:
extensions = [".bam", ".sam", ".sam.gz"]
files = brenninc_utils.find_files(sam_filename,
extensions=extensions,
recursive=True)
(features, counts) = get_features(gff_filename, stranded, feature_type,
id_attribute, quiet)
for a_file in files:
print "counting", a_file
count_reads_using_features(a_file, features, counts, samtype, order,
stranded, overlap_mode, quiet, minaqual,
samout, directory)
def test_txt(self):
fileList = brenninc_utils.find_files(os.getcwd(), extensions="txt")
found = check_files_for_ending(fileList, "brenninc_utils_test.py")
self.assertFalse(found)
def pathsort(path, outputdir=None, qual_scale=_default_qual_scale):
files = brenninc_utils.find_files(path, ["fastq", "fastq.gz"])
for afile in files:
sort(fastq_file=afile, outputdir=outputdir, qual_scale=qual_scale)
def count_alignments(path=os.getcwd(), output_file=None):
files = brenninc_utils.find_files(path, ['sam', 'sam.gz'])
with brenninc_utils.smart_open(output_file) as handle:
for sam_file in files:
count_single_file(sam_file, handle)
def makehead(path, sequences=100, outputdir=None,
qual_scale=_default_qual_scale):
files = brenninc_utils.find_files(path, ["fastq", "fastq.gz"])
for afile in files:
head(path=afile, sequences=sequences, outputdir=outputdir,
qual_scale=qual_scale)
def count_alignments(path=os.getcwd(), output_file=None):
files = brenninc_utils.find_files(path, ['sam', 'sam.gz'])
with brenninc_utils.smart_open(output_file) as handle:
for sam_file in files:
count_single_file(sam_file, handle)
def test_parent(self):
parent = os.path.dirname(os.getcwd())
fileList = brenninc_utils.find_files(parent)
found = check_files_for_ending(fileList, "brenninc_utils_test.py")
self.assertFalse(found)
def test_parent_recursive(self):
parent = os.path.dirname(os.getcwd())
fileList = brenninc_utils.find_files(parent, recursive=True)
found = check_files_for_ending(fileList, "brenninc_utils_test.py")
self.assertTrue(found)
def test_all(self):
fileList = brenninc_utils.find_files(os.getcwd())
found = check_files_for_ending(sorted(fileList), "brenninc_utils_test.py")
self.assertTrue(found)
def test_txt_py(self):
fileList = brenninc_utils.find_files(os.getcwd(),
extensions=["txt", ".py"])
found = check_files_for_ending(fileList, "brenninc_utils_test.py")
self.assertTrue(found)
def test_all(self):
fileList = brenninc_utils.find_files(os.getcwd())
found = check_files_for_ending(sorted(fileList),
"brenninc_utils_test.py")
self.assertTrue(found)
def test_parent_recursive(self):
parent = os.path.dirname(os.getcwd())
fileList = brenninc_utils.find_files(parent, recursive=True)
found = check_files_for_ending(fileList, "brenninc_utils_test.py")
self.assertTrue(found)
def test_parent(self):
parent = os.path.dirname(os.getcwd())
fileList = brenninc_utils.find_files(parent)
found = check_files_for_ending(fileList, "brenninc_utils_test.py")
self.assertFalse(found)
def test_txt_py(self):
fileList = brenninc_utils.find_files(os.getcwd(), extensions=["txt", ".py"])
found = check_files_for_ending(fileList, "brenninc_utils_test.py")
self.assertTrue(found)
def test_txt(self):
fileList = brenninc_utils.find_files(os.getcwd(), extensions="txt")
found = check_files_for_ending(fileList, "brenninc_utils_test.py")
self.assertFalse(found)
