def plot(meme_dir, centrimo_dir, fimo_dir_sample, fimo_dir_control, name,
flank_motif, motif, oc, configuration, show_progress, genome_build):
"""Create stacked conservation plots"""
if not oc:
moca_out_dir = os.path.join(os.getcwd(), 'moca_output')
else:
moca_out_dir = oc
if show_progress:
progress_bar = ProgressBar(['Creating Plots']*len(conservation_wig_keys))
moca_pipeline = pipeline.Pipeline(configuration)
meme_file = os.path.join(meme_dir, 'meme.txt')
genome_data = moca_pipeline.get_genome_data(genome_build)
wigfiles = {}
for key in list(conservation_wig_keys):
try:
wigfiles[key] = genome_data['{}_wig'.format(key)]
except KeyError:
pass
fimo_control= os.path.join(fimo_dir_control, 'fimo.txt')
fimo_sample = os.path.join(fimo_dir_sample, 'fimo.txt')
safe_makedir(moca_out_dir)
main_intervals = get_start_stop_intervals(fimo_sample, flank_length=flank_motif)
random_intervals = get_start_stop_intervals(fimo_control, flank_length=flank_motif)
sample_score_files = []
control_score_files = []
for key in list(conservation_wig_keys):
wigfile = wigfiles[key]
if show_progress:
progress_bar.show_progress('Creating plots')
sample_score_file = moca_pipeline.save_conservation_scores(main_intervals, wigfile,
fimo_dir_sample, out_prefix=key)
control_score_file = moca_pipeline.save_conservation_scores(random_intervals, wigfile,
fimo_dir_control, out_prefix=key)
sample_score_files.append(sample_score_file)
control_score_files.append(control_score_file)
create_plot(meme_file,
name,
output_dir=moca_out_dir,
centrimo_dir=centrimo_dir,
motif_number=motif,
flank_length=flank_motif,
sample_score_files=[sample_score_file],
control_score_files=[control_score_file],
reg_plot_titles=[key.capitalize() for key in list(conservation_wig_keys)],
annotate=None)
def find_motifs(bedfile, oc, configuration, slop_length,
flank_motif, n_motif, cores, genome_build, show_progress):
"""Run meme to locate motifs and create conservation stacked plots"""
root_dir = os.path.dirname(os.path.abspath(bedfile))
if not oc:
moca_out_dir = os.path.join(os.getcwd(), 'moca_output')
else:
moca_out_dir = oc
moca_pipeline = pipeline.Pipeline(configuration)
genome_data = moca_pipeline.get_genome_data(genome_build)
genome_fasta = genome_data['fasta']
genome_table = genome_data['genome_table']
wigfiles = {}
for key in list(conservation_wig_keys):
try:
wigfiles[key] = genome_data['{}_wig'.format(key)]
except KeyError:
pass
safe_makedir(moca_out_dir)
bedfile_fn, _ = filename_extension(bedfile)
if show_progress:
msg_list = ['Extracting Fasta',
'Running MEME',
'Running CENTRIMO']
msg_list_e = ['Generating random Fasta', 'Running fimo random', 'Running fimo main'] + ['Extracting Scores']*len(wigfiles.keys()) + ['Creating PLot']
msg_list = msg_list + msg_list_e*n_motif
progress_bar = ProgressBar(msg_list)
query_train_fasta = os.path.join(moca_out_dir,
bedfile_fn + '_train_flank_{}.fasta'.format(slop_length))
query_test_fasta = os.path.join(moca_out_dir,
bedfile_fn + '_test_flank_{}.fasta'.format(slop_length))
if show_progress:
progress_bar.show_progress('Extracting Fasta')
bed_o = bedoperations.Bedfile(bedfile, genome_table, moca_out_dir)
bed_train, bed_test = bed_o.split_train_test_bed(train_peaks_count=500, test_peaks_count=500)
bed_train_slopped = bed_o.slop_bed(bed_train, flank_length=slop_length)
bed_test_slopped = bed_o.slop_bed(bed_test, flank_length=slop_length)
bed_o.extract_fasta(bed_train_slopped, fasta_in=genome_fasta, fasta_out=query_train_fasta)
bed_o.extract_fasta(bed_test_slopped, fasta_in=genome_fasta, fasta_out=query_test_fasta)
#memechip_out_dir = os.path.join(moca_out_dir, 'memechip_analysis')
meme_out_dir = os.path.join(moca_out_dir, 'meme_out')
memechip_out_dir = meme_out_dir
meme_params = moca_pipeline.get_meme_default_params
if cores==1:
re.sub(r' -p*', '', meme_params)
else:
re.sub(r'-p*', '-p {}'.format(cores), meme_params)
if show_progress:
progress_bar.show_progress('Running MEME')
#meme_run_out = moca_pipeline.run_memechip(fasta_in=query_fasta, out_dir=memechip_out_dir)
#
meme_run_out = moca_pipeline.run_meme(fasta_in=query_train_fasta,
out_dir=meme_out_dir,
strargs=meme_params)
if meme_run_out['stderr']!='':
sys.stdout.write('Error running MEME: {}'.format(meme_run_out['stderr']))
sys.exit(1)
meme_file = os.path.join(meme_out_dir, 'meme.txt')
meme_summary = read_memefile(meme_file)
if show_progress:
progress_bar.show_progress('Running CENTRIMO')
centrimo_main_dir = os.path.join(moca_out_dir, 'centrimo_out')
centrimo_main = moca_pipeline.run_centrimo(meme_file=meme_file,
fasta_in=query_test_fasta,
out_dir=centrimo_main_dir)
for motif in range(1, meme_summary['total_motifs']+1):
fimo_rand_dir = os.path.join(memechip_out_dir, 'fimo_random_{}'.format(motif))
fimo_main_dir = os.path.join(memechip_out_dir, 'fimo_out_{}'.format(motif))
safe_makedir(fimo_rand_dir)
random_fasta = os.path.join(fimo_rand_dir, 'random_{}.fa'.format(motif))
if show_progress:
progress_bar.show_progress('Generating Random Fasta: {}'.format(motif))
moca_pipeline.run_fasta_shuffler(fasta_in=query_train_fasta, fasta_out=random_fasta)
#Random
if show_progress:
progress_bar.show_progress('Running FIMO Random')
fimo_rand = moca_pipeline.run_fimo(motif_file=meme_file,
motif_num=motif,
sequence_file=random_fasta,
out_dir=fimo_rand_dir)
#Main
if show_progress:
progress_bar.show_progress('Running FIMO Main')
fimo_main = moca_pipeline.run_fimo(motif_file=meme_file,
motif_num=motif,
sequence_file=query_test_fasta,
out_dir=fimo_main_dir)
fimo_rand_file = os.path.join(fimo_rand_dir, 'fimo.txt')
fimo_main_file = os.path.join(fimo_main_dir, 'fimo.txt')
main_intervals = get_start_stop_intervals(fimo_main_file, flank_length=flank_motif)
random_intervals = get_start_stop_intervals(fimo_rand_file, flank_length=flank_motif)
sample_score_files = []
control_score_files = []
for key in list(conservation_wig_keys):
wigfile = wigfiles[key]
if show_progress:
progress_bar.show_progress('Creating plots')
sample_score_file = moca_pipeline.save_conservation_scores(main_intervals, wigfile,
fimo_main_dir, out_prefix=key)
control_score_file = moca_pipeline.save_conservation_scores(random_intervals, wigfile,
fimo_rand_dir, out_prefix=key)
sample_score_files.append(sample_score_file)
control_score_files.append(control_score_file)
if show_progress:
progress_bar.show_progress('Creating Plot')
create_plot(meme_file,
bedfile_fn,
output_dir=moca_out_dir,
centrimo_dir=centrimo_main_dir,
motif_number=motif,
flank_length=flank_motif,
sample_score_files=sample_score_files,
control_score_files=control_score_files,
reg_plot_titles=[key.capitalize() for key in list(conservation_wig_keys)],
annotate=None)
if show_progress:
progress_bar.close()