def new_bamm_job(next_id, example_file, peng_job):
job_info, next_id = new_example_job_info(next_id, 'bamm', example_file)
job_info.save()
mdb = get_object_or_404(MotifDatabase, db_id=EXAMPLE_MOTIF_DB)
bamm_job = BaMMJob(
meta_job=job_info,
Motif_Initialization="Custom File",
Motif_Init_File_Format="PWM",
MMcompare=True,
score_Seqset=True,
FDR=True,
peng_job=peng_job,
motif_db=mdb,
)
with open(example_file) as fh:
bamm_job.Input_Sequences.save(os.path.basename(example_file), File(fh))
n_motifs = 3
meme_file = path.join(get_job_output_folder(peng_job.pk),
FILTERPWM_OUTPUT_FILE)
motifs = get_motif_ids(meme_file)[:n_motifs]
save_selected_motifs(motifs, peng_job.pk, bamm_job.meta_job.pk)
copy_peng_to_bamm(peng_job.pk, bamm_job.pk, motifs)
bamm_job.num_init_motifs = len(motifs)
bamm_job.num_motifs = len(motifs)
bamm_job.Motif_InitFile.name = get_motif_init_file(str(bamm_job.pk))
bamm_job.Motif_Initialization = "Custom File"
bamm_job.Motif_Init_File_Format = "PWM"
bamm_job.score_Cutoff = 0.0001
bamm_job.save()
bamm_refinement_pipeline.delay(bamm_job.meta_job.pk)
while not job_info.complete:
job_info = get_object_or_404(JobInfo, pk=job_info.pk)
time.sleep(10)
return next_id, bamm_job.pk
def new_mmcompare_job(next_id, example_file, bamm_id):
job_info, next_id = new_example_job_info(next_id, 'compare', example_file)
job_info.save()
mdb = get_object_or_404(MotifDatabase, db_id=EXAMPLE_MOTIF_DB)
mmcompare_job = MMcompareJob(meta_job=job_info,
motif_db=mdb,
Motif_Init_File_Format="PWM"
# Fill in missing data
)
# Init motif_init_file
motif_init_file_src = get_motif_init_file(str(bamm_id))
motif_init_file_dst = mmcompare_motif_init_file(str(mmcompare_job.pk))
motif_init_directory = os.path.splitext(motif_init_file_dst)[0]
if not os.path.exists(motif_init_directory):
os.makedirs(motif_init_directory)
copyfile(motif_init_file_src, motif_init_file_dst)
init_bname = path.basename(motif_init_file_dst)
mmcompare_job.Motif_InitFile = filename_relative_to_job_dir(
mmcompare_job, init_bname)
mmcompare_job.save()
mmcompare_pipeline.delay(mmcompare_job.meta_job.pk)
while not job_info.complete:
job_info = get_object_or_404(JobInfo, pk=job_info.pk)
time.sleep(10)
return next_id
def copy_peng_to_bamm(peng_id, bamm_id, selected_motifs):
bamm_output_dir = path.join(get_job_output_folder(bamm_id), PENG_OUTPUT)
bamm_plot_output_directory = path.join(bamm_output_dir, MEME_PLOT_DIRECTORY)
if not path.exists(bamm_plot_output_directory):
os.makedirs(bamm_plot_output_directory)
# copy meme.out
meme_path_src = os.path.join(peng_meme_directory(peng_id), MEME_OUTPUT_FILE)
meme_path_dst = get_motif_init_file(str(bamm_id))
meme_drop_unselected_motifs(meme_path_src, meme_path_dst, selected_motifs)
# copy results of filterPWM
filterpwm_src = os.path.join(get_job_output_folder(peng_id), FILTERPWM_OUTPUT_FILE)
logger.debug('copying %s -> %s', filterpwm_src, bamm_output_dir)
shutil.copy(filterpwm_src, bamm_output_dir)
# copy input file
peng_input = os.path.join(get_job_input_folder(peng_id))
bamm_input = os.path.join(get_job_input_folder(bamm_id))
if not path.exists(bamm_input):
os.makedirs(bamm_input)
# TODO: Is this supposed to be multiple files??
for file in os.listdir(peng_input):
logger.debug('copying %s -> %s', filterpwm_src, bamm_output_dir)
src = os.path.join(peng_input, file)
shutil.copy(src, bamm_input)
def new_bammscan_job(next_id, example_file, bamm_id):
job_info, next_id = new_example_job_info(next_id, 'scan', example_file)
job_info.save()
mdb = get_object_or_404(MotifDatabase, db_id=EXAMPLE_MOTIF_DB)
bamm_scan_job = BaMMScanJob(
meta_job=job_info,
motif_db=mdb,
MMcompare=True,
Motif_Init_File_Format="PWM",
)
with open(example_file) as fh:
bamm_scan_job.Input_Sequences.save(os.path.basename(example_file),
File(fh))
bamm_scan_job.Motif_InitFile.name = get_motif_init_file(str(bamm_id))
bamm_scan_job.score_Cutoff = 0.0001
bamm_scan_job.save()
bamm_scan_pipeline.delay(bamm_scan_job.meta_job.pk)
while not job_info.complete:
job_info = get_object_or_404(JobInfo, pk=job_info.pk) # Kind of dirt.
time.sleep(10)
return next_id
def peng_to_bamm_result_detail(request, pk):
result = get_object_or_404(BaMMJob, meta_job__pk=pk)
meta_job = result.meta_job
relative_result_folder = get_result_folder(pk)
job_output_dir = get_job_output_folder(pk)
peng_path = path.join(job_output_dir, "pengoutput")
meme_plots = path.join(job_output_dir, "pengoutput", "meme_plots")
meme_motifs = load_meme_ids(peng_path)
#meme_meta_info_list = Meme.fromfile(os.path.join(peng_path, "out.meme"))
meme_meta_info_list = Meme.fromfile(get_motif_init_file(str(meta_job.job_id)))
motif_db = result.motif_db
db_dir = motif_db.relative_db_model_dir
if meta_job.complete:
num_logos = range(1, (min(2, result.model_order)+1))
return render(request, 'bamm/bamm_result_detail.html', {
'result': result, 'opath': get_result_folder(pk),
'mode': meta_job.mode,
'Output_filename': result.filename_prefix,
'num_logos': num_logos,
'db_dir': db_dir,
'meme_logo_path': path.relpath(meme_plots, relative_result_folder),
'meme_motifs': meme_motifs,
'meme_meta_info': meme_meta_info_list,
})
else:
log_file = get_log_file(pk)
command = "tail -20 %r" % log_file
output = os.popen(command).read()
return render(request, 'results/result_status.html', {
'output': output,
'job_id': meta_job.pk,
'job_name': meta_job.job_name,
'status': meta_job.status
})