def main():
# Parse the command line inputs
parser = argparse.ArgumentParser(description="map_reads")
parser.add_argument("-settings",
dest="settings",
required=True,
help="settings.txt",
metavar="string")
parser.add_argument("-samples",
dest="samples",
required=True,
help="1,2",
metavar="string")
parser.add_argument("-cores",
dest="cores",
required=True,
help="# cores",
metavar="int")
args = parser.parse_args()
# Run the command
samples = args.samples.split(',')
settings = ga.load_settings(args.settings)
cores = args.cores
for s in samples:
status = ga.map_reads(settings, s, cores)
return status
def main():
# Parse the command line inputs
parser = argparse.ArgumentParser(description="transcription_profile")
parser.add_argument("-settings",
dest="settings",
required=True,
help="settings.txt",
metavar="string")
parser.add_argument("-samples",
dest="samples",
required=True,
help="1,2",
metavar="string")
parser.add_argument("-chroms",
dest="chroms",
required=True,
help="1,2",
metavar="string")
args = parser.parse_args()
# Run the command
samples = args.samples.split(',')
chroms = args.chroms.split(',')
settings = ga.load_settings(args.settings)
for s in samples:
ga.create_profiles(settings, s, chroms, scale=10e-5)
def main():
# Parse the command line inputs
parser = argparse.ArgumentParser(description="count_reads")
parser.add_argument("-settings",
dest="settings",
required=True,
help="settings.txt",
metavar="string")
parser.add_argument("-samples",
dest="samples",
required=True,
help="1,2",
metavar="string")
parser.add_argument("-attribute",
dest="attribute",
required=False,
metavar="string",
default='name')
parser.add_argument("-strand_opt",
dest="strand_opt",
required=False,
help="If stranded protocol was used",
metavar="string",
default='reverse')
parser.add_argument("-cores",
dest="cores",
required=True,
help="# cores",
metavar="int")
args = parser.parse_args()
# Run the command
cores = args.cores
samples = args.samples.split(',')
settings = ga.load_settings(args.settings)
attribute = args.attribute
s_opt = args.strand_opt
for s in samples:
features = ga.load_features(settings, s)
status1 = ga.mapped_reads(settings, s, cores)
status2 = ga.gene_lengths(settings, s)
for f in features:
status3 = ga.count_reads(settings,
s,
feature=f,
attribute=attribute,
strand_opt=s_opt)
if status3 == 0:
continue
else:
return "Count reads failed"
return (status1 + status2)
def main():
# Parse the command line inputs
parser = argparse.ArgumentParser(description="part_profile_analysis")
parser.add_argument("-settings",
dest="settings",
required=True,
help="settings.txt",
metavar="string")
args = parser.parse_args()
settings = ga.load_settings(args.settings)
samples = []
for s in settings.keys():
if s != 'None':
samples.append(s)
chr_promoters = ga.characterize_promoter_units(
settings,
s,
upstream_bp=10,
downstream_skip_bp=0,
downstream_bp=10,
normed=True)
ga.save_characterization_data(settings,
s,
chr_promoters,
part_type='promoter')
chr_terminators = ga.characterize_terminators(settings,
s,
upstream_bp=10,
upstream_skip_bp=0,
downstream_bp=10,
normed=True)
ga.save_characterization_data(settings,
s,
chr_terminators,
part_type='terminator')
chr_ribozymes = ga.characterize_ribozymes(settings,
s,
upstream_promoter_bp=10,
upstream_bp=10,
downstream_skip_bp=0,
downstream_bp=10,
normed=True)
ga.save_characterization_data(settings,
s,
chr_ribozymes,
part_type='ribozyme')
ga.combine_promoter_characterizations(settings, samples)
ga.combine_terminator_characterizations(settings, samples)
ga.combine_ribozyme_characterizations(settings, samples)
def main():
# Parse the command line inputs
parser = argparse.ArgumentParser(description="profile_normalization")
parser.add_argument("-settings",
dest="settings",
required=True,
help="settings.txt",
metavar="string")
parser.add_argument("-samples",
dest="samples",
required=True,
help="1,2",
metavar="string")
args = parser.parse_args()
# Run the command
samples = args.samples.split(',')
settings = ga.load_settings(args.settings)
for s in samples:
ga.normalise_profiles(settings, s, correction=False, baseline_us_bp=10)
def main():
# Parse the command line inputs
parser = argparse.ArgumentParser(description="fragment_distributions")
parser.add_argument("-settings",
dest="settings",
required=True,
help="settings.txt",
metavar="string")
parser.add_argument("-samples",
dest="samples",
required=True,
help="1,2",
metavar="string")
args = parser.parse_args()
# Run the command
samples = args.samples.split(',')
settings = ga.load_settings(args.settings)
for s in samples:
ga.fragment_length_dists(settings, s, reads_to_sample=1000000)
def main():
# Parse the command line inputs
parser = argparse.ArgumentParser(description="de_analysis")
parser.add_argument("-settings",
dest="settings",
required=True,
help="settings.txt",
metavar="string")
parser.add_argument("-group1",
dest="group1",
required=True,
help="1,2,6,7",
metavar="string")
parser.add_argument("-group2",
dest="group2",
required=True,
help="3,4,8,9",
metavar="string")
parser.add_argument("-output_prefix",
dest="output_prefix",
required=True,
help="WT_vs_Sample",
metavar="string")
parser.add_argument("-bin_path",
dest="bin_path",
required=True,
help="/usr/bin/",
metavar="string")
args = parser.parse_args()
# Run the command
settings = ga.load_settings(args.settings)
cur_group1 = args.group1
cur_group2 = args.group2
cur_output_prefix = args.output_prefix
cur_bin_path = args.bin_path
# Run the DE analysis
ga.de_analysis(settings,
cur_group1,
cur_group2,
cur_output_prefix,
bin_path=cur_bin_path)
def main():
# Parse the command line inputs
parser = argparse.ArgumentParser(description="count_reads")
parser.add_argument("-settings",
dest="settings",
required=True,
help="settings.txt",
metavar="string")
parser.add_argument("-samples",
dest="samples",
required=True,
help="1,2",
metavar="string")
parser.add_argument("-feature",
dest="feature",
required=True,
help="gene",
metavar="string")
parser.add_argument("-attribute",
dest="attribute",
required=True,
help="Name",
metavar="string")
parser.add_argument("-strand_opt",
dest="strand_opt",
required=True,
help="no/yes/reverse",
metavar="string")
args = parser.parse_args()
# Run the command
samples = args.samples.split(',')
settings = ga.load_settings(args.settings)
f = args.feature
a = args.attribute
s_opt = args.strand_opt
for s in samples:
ga.count_reads(settings, s, feature=f, attribute=a, strand_opt=s_opt)
ga.gene_lengths(settings, s, feature=f, attribute=a)
ga.mapped_reads(settings, s)
def main():
# Parse the command line inputs
parser = argparse.ArgumentParser(description="read_analysis")
parser.add_argument("-settings",
dest="settings",
required=True,
help="settings.txt",
metavar="string")
parser.add_argument("-bin_path",
dest="bin_path",
required=True,
help="/usr/bin/",
metavar="string")
args = parser.parse_args()
# Run the command
settings = ga.load_settings(args.settings)
cur_bin_path = args.bin_path
# Collate read counts and mapped reads for all samples
counts = {}
mapped_reads = {}
sample_names = []
gene_lengths = {}
for s in sorted(settings.keys()):
if s != 'None':
sample_names.append(s)
counts[s] = ga.read_count_file(ga.count_filename(settings, s))
mapped_reads[s] = ga.load_mapped_reads(settings, s)
gene_lengths[s] = ga.load_gene_lengths(settings, s)
count_matrix = ga.combine_counts(counts, sample_names)
ga.save_count_matrix(count_matrix, sample_names,
ga.count_matrix_filename(settings))
ga.save_mapped_reads_matrix(mapped_reads, sample_names,
ga.mapped_reads_matrix_filename(settings))
ga.save_gene_length_matrix(gene_lengths,
ga.gene_length_matrix_filename(settings))
# Generate normalisation factors (edgeR) and output RPKM/FPKM values
ga.norm_fpkm(settings, bin_path=cur_bin_path)