def get_chapter(driver, root_url, chapter_num, manga_name):
chapter_url = f'{root_url}/{chapter_num}'
path = f'{home}/Downloads/Manga/{manga_name}/Chapter_{chapter_num}/'
create_dir(path)
# get all pages
page_num = 1
img_srcs = []
print(f'getting chapter {chapter_num}...')
with concurrent.futures.ThreadPoolExecutor() as executor:
while True:
future = executor.submit(get_page, driver, chapter_url, page_num,
chapter_num, manga_name, path)
result = future.result()
if result == '404':
break
elif result == 'unknow_error':
continue
else:
img_srcs.append(result)
page_num += 1
print(f'chapter {chapter_num} successfully getted!')
def main():
options = docopt(__doc__)
command_log = 'fast_circ.py parameters: ' + ' '.join(sys.argv)
work_dir = options['--output']
if work_dir != '.' and 'work_dir' != './':
create_dir(work_dir)
if options['parse']:
# parse fusion reads from <fusion> file
options['--bed'] = '%s/back_spliced_junction.bed' % work_dir
parse_command(options, command_log)
# annotate circular RNAs
options['--output'] = '%s/circularRNA_known.txt' % options['--output']
annotate_command(options, command_log)
elif options['annotate']:
# align fusion reads
options['--output'] = '%s/alignment' % work_dir
options['--bed'] = '%s/back_spliced_junction.bed' % work_dir
align_command(options, command_log)
# annotate circular RNAs
options['--output'] = '%s/circularRNA_known.txt' % options['--output']
annotate_command(options, command_log)
elif options['denovo']:
# align fusion reads
options['--output'] = '%s/alignment' % work_dir
options['--bed'] = '%s/back_spliced_junction.bed' % work_dir
align_command(options, command_log)
# de novo assemble circular RNAs
options['--tophat'] = '%s/alignment/tophat' % work_dir
options['--output'] = '%s/assemble' % work_dir
assemble_command(options, command_log)
# fetch AS events of circular RNAs
options['--output'] = '%s/denovo' % work_dir
options['--abs'] = '%s/abs' % work_dir
denovo_command(options, work_dir, command_log)
def download_manga_from_list():
with open('download_list.json', 'r') as file:
manga_data = json.load(file)
manga_name = manga_data['manga_name']
chapters = manga_data['chapters']
home = get_home_dir()
for chapter in chapters:
chapter_id = list(chapter.keys())[0]
chapter_imgs = list(chapter.values())[0]
path = f'{home}/Downloads/Manga/{manga_name}/{chapter_id}/'
create_dir(path)
num = 1
chapter_number = chapter_id.split('_')[1]
print(f'Downloading chapter {chapter_number}...')
with concurrent.futures.ThreadPoolExecutor() as executor:
for img in chapter_imgs:
executor.submit(download_img, img, path, num)
num += 1
print(f'Chapter {chapter_number} Downloaded!\n')
def assemble(options):
# check output directory
out_dir = create_dir(options['--output'])
# check tophat results
tophat_dir = options['--tophat']
# check cufflinks
if which('cufflinks') is None:
sys.exit('Cufflinks is required for CIRCexplorer2 assemble!')
# check genePredToGtf
if which('genePredToGtf') is None:
sys.exit('genePredToGtf is required for CIRCexplorer2 assemble!')
# check gtfToGenePred
if which('gtfToGenePred') is None:
sys.exit('gtfToGenePred is required for CIRCexplorer2 assemble!')
# prepare cufflinks directory
cufflinks_dir = out_dir
create_dir(cufflinks_dir)
# filter ref file
ref_filter(options['--ref'], tophat_dir, cufflinks_dir)
# assemble with cufflinks
cufflinks_assemble(tophat_dir, cufflinks_dir, options['--thread'],
options['--remove-rRNA'], options['--max-bundle-frags'])
# convert assembly results
convert_assembly_gtf(tophat_dir, cufflinks_dir, options['--ref'],
options['--bb'], options['--chrom-size'])
def annotate(options):
# check output directory
out_dir = check_dir(options['<circ_dir>'])
# prepare annotate directory
annotate_dir = '%s/annotate' % out_dir
create_dir(annotate_dir)
# annotate fusion junctions
annotate_fusion(options['--ref'], annotate_dir)
# fix fusion juncrions
fix_fusion(options['--ref'], options['--genome'], annotate_dir,
options['--no-fix'])
def annotate(options):
# check output directory
out_dir = check_dir(options['<circ_dir>'])
# prepare annotate directory
annotate_dir = '%s/annotate' % out_dir
create_dir(annotate_dir)
# annotate fusion junctions
annotate_fusion(options['--ref'], annotate_dir)
# fix fusion juncrions
fix_fusion(options['--ref'], options['--genome'], annotate_dir,
options['--no-fix'])
def denovo(options):
# check output directory
out_dir = check_dir(options['<circ_dir>'])
# check tophat results
if options['--tophat-dir']:
tophat_dir = check_dir(options['--tophat-dir'])
else:
tophat_dir = check_dir(out_dir + '/tophat')
# prepare denovo directory
denovo_dir = '%s/denovo' % out_dir
create_dir(denovo_dir)
# combine ref files
cufflinks_ref_path = '%s/cufflinks/transcripts_ref.txt' % out_dir
if os.path.isfile(cufflinks_ref_path):
print('Combine %s with %s to create a new ref file!' %
(options['--ref'], cufflinks_ref_path))
ref_path = '%s/combined_ref.txt' % denovo_dir
new_ref_f = open(ref_path, 'w')
with open(cufflinks_ref_path, 'r') as cuff_ref:
for line in cuff_ref:
if line.startswith('CUFF'): # only import novel isoforms
new_ref_f.write(line)
new_ref_f.write(open(options['--ref'], 'r').read())
new_ref_f.close()
else:
print('Warning: no cufflinks directory under %s!' % out_dir)
print('Please run CIRCexplorer2 assembly before this step!')
ref_path = options['--ref']
# annotate fusion junctions
annotate_fusion(ref_path, denovo_dir, denovo_flag=1)
# fix fusion juncrions
fix_fusion(ref_path,
options['--genome'],
denovo_dir,
options['--no-fix'],
denovo_flag=1)
# extract novel circRNAs
extract_novel_circ(denovo_dir, options['--ref'])
if options['--as']:
if options['--pAplus'] and os.path.isdir(options['--pAplus']):
pAplus_dir = os.path.abspath(options['--pAplus'])
else:
sys.exit('You should offer --pAplus option in --as mode!')
if not options['--as-type'] or options['--as-type'] == 'CE':
# extract cassette exons
extract_cassette_exon(denovo_dir, tophat_dir, pAplus_dir,
options['--rpkm'])
if not options['--as-type'] or options['--as-type'] == 'RI':
# extract retained introns
extract_retained_intron(denovo_dir, tophat_dir, pAplus_dir)
if not options['--as-type'] or options['--as-type'] == 'ASS':
# characterize A5SS and A3SS
parse_splice_site(denovo_dir, tophat_dir, pAplus_dir)
def denovo(options):
# check output directory
out_dir = check_dir(options['<circ_dir>'])
# check tophat results
if options['--tophat-dir']:
tophat_dir = check_dir(options['--tophat-dir'])
else:
tophat_dir = check_dir(out_dir + '/tophat')
# prepare denovo directory
denovo_dir = '%s/denovo' % out_dir
create_dir(denovo_dir)
# combine ref files
cufflinks_ref_path = '%s/cufflinks/transcripts_ref.txt' % out_dir
if os.path.isfile(cufflinks_ref_path):
print('Combine %s with %s to create a new ref file!' %
(options['--ref'], cufflinks_ref_path))
ref_path = '%s/combined_ref.txt' % denovo_dir
new_ref_f = open(ref_path, 'w')
with open(cufflinks_ref_path, 'r') as cuff_ref:
for line in cuff_ref:
if line.startswith('CUFF'): # only import novel isoforms
new_ref_f.write(line)
new_ref_f.write(open(options['--ref'], 'r').read())
new_ref_f.close()
else:
print('Warning: no cufflinks directory under %s!' % out_dir)
print('Please run CIRCexplorer2 assembly before this step!')
ref_path = options['--ref']
# annotate fusion junctions
annotate_fusion(ref_path, denovo_dir, 1)
# fix fusion juncrions
fix_fusion(ref_path, options['--genome'], denovo_dir,
options['--no-fix'], 1)
# extract novel circRNAs
extract_novel_circ(denovo_dir, options['--ref'])
if options['--as']:
if options['--pAplus'] and os.path.isdir(options['--pAplus']):
pAplus_dir = os.path.abspath(options['--pAplus'])
else:
sys.exit('You should offer --pAplus option in --as mode!')
if not options['--as-type'] or options['--as-type'] == 'CE':
# extract cassette exons
extract_cassette_exon(denovo_dir, tophat_dir, pAplus_dir,
options['--rpkm'])
if not options['--as-type'] or options['--as-type'] == 'RI':
# extract retained introns
extract_retained_intron(denovo_dir, tophat_dir, pAplus_dir)
if not options['--as-type'] or options['--as-type'] == 'ASS':
# characterize A5SS and A3SS
parse_splice_site(denovo_dir, tophat_dir, pAplus_dir)
def check_outdir(out_dir):
'''
1. Clear output directory if not empty
2. Create essential subdirectories
'''
print('Check output directory...')
# clear output directory if not empty
create_dir(out_dir)
dir_path = os.path.abspath(out_dir)
# create essential subdirectories
os.mkdir(dir_path + '/bowtie1_index')
os.mkdir(dir_path + '/bowtie2_index')
os.mkdir(dir_path + '/tophat')
os.mkdir(dir_path + '/tophat_fusion')
return dir_path
def check_outdir(out_dir):
'''
1. Clear output directory if not empty
2. Create essential subdirectories
'''
print('Check output directory...')
# clear output directory if not empty
create_dir(out_dir)
dir_path = os.path.abspath(out_dir)
# create essential subdirectories
os.mkdir(dir_path + '/bowtie1_index')
os.mkdir(dir_path + '/bowtie2_index')
os.mkdir(dir_path + '/tophat')
os.mkdir(dir_path + '/tophat_fusion')
return dir_path
def parse(options):
aliger = set(['STAR', 'MapSplice', 'segemehl'])
if options['-t'] not in aliger:
sys.exit('Error: CIRCexplorer2 parse does not support %s!' %
options['-t'])
# check output directory
create_dir(options['--output'])
out_dir = os.path.abspath(options['--output'])
out = out_dir + '/fusion_junction.bed'
# parse fusion junctions from other aligers
if options['-t'] == 'STAR':
star_parse(options['<fusion>'], out)
elif options['-t'] == 'MapSplice':
mapsplice_parse(options['<fusion>'], out)
elif options['-t'] == 'segemehl':
segemehl_parse(options['<fusion>'], out)
def parse(options):
aliger = set(['STAR', 'MapSplice', 'segemehl'])
if options['-t'] not in aliger:
sys.exit('Error: CIRCexplorer2 parse does not support %s!' %
options['-t'])
# check output directory
create_dir(options['--output'])
out_dir = os.path.abspath(options['--output'])
out = out_dir + '/fusion_junction.bed'
# parse fusion junctions from other aligers
if options['-t'] == 'STAR':
star_parse(options['<fusion>'], out)
elif options['-t'] == 'MapSplice':
mapsplice_parse(options['<fusion>'], out)
elif options['-t'] == 'segemehl':
segemehl_parse(options['<fusion>'], out)
def hisat_to_tophat(bam_f, denovo_dir):
if which('regtools') is None:
sys.exit('regtools is required "as" analysis when use hisat2 mapping \
results!')
o_dir = create_dir('%s/temp%f' % (denovo_dir, time.time()))
os.symlink(os.path.realpath(bam_f), "%s/accepted_hits.bam" % o_dir)
pysam.index("%s/accepted_hits.bam" % o_dir)
# creat junctions.bed file
regtools_cmd = 'regtools junctions extract -s 0 '
regtools_cmd += '-o %s %s' % ("%s/junctions.bed" % o_dir,
"%s/accepted_hits.bam" % o_dir)
regtools_cmd += ' 2> %s/regtools.log' % o_dir
print('Creating junctions.bed command:')
print(regtools_cmd)
return_code = os.system(regtools_cmd) >> 8
if return_code:
sys.exit('Error: cannot create junctions.bed file!')
return o_dir
def denovo(options):
# check tophat results
# if options['--tophat']:
# tophat_dir = check_dir(options['--tophat'])
# prepare denovo directory
denovo_dir = options['--output']
create_dir(denovo_dir)
# combine ref files
cufflinks_ref_path = '%s/transcripts_ref.txt' % options['--cuff']
if os.path.isfile(cufflinks_ref_path):
print('Combine %s with %s to create a new ref file!' %
(options['--ref'], cufflinks_ref_path))
ref_path = '%s/combined_ref.txt' % denovo_dir
new_ref_f = open(ref_path, 'w')
with open(cufflinks_ref_path, 'r') as cuff_ref:
for line in cuff_ref:
if line.startswith('CUFF'): # only import novel isoforms
new_ref_f.write(line)
new_ref_f.write(open(options['--ref'], 'r').read())
new_ref_f.close()
else:
print('Warning: no cufflinks directory %s!' % options['--cuff'])
print('Please run CIRCexplorer2 assembly before this step!')
ref_path = options['--ref']
# create temporary annotated fusion file
fusion_tmp = tempfile.TemporaryFile(mode='w+')
# annotate fusion junctions
annotate_fusion(ref_path, options['--bed'], fusion_tmp, denovo_flag=1)
# fix fusion juncrions
out_f = '%s/circularRNA_full.txt' % denovo_dir
fix_fusion(ref_path, options['--genome'], fusion_tmp, out_f,
options['--no-fix'], denovo_flag=1)
# extract novel circRNAs
extract_novel_circ(denovo_dir, options['--ref'])
if options['--as']:
create_dir(options['--as'])
if options['--pAplus'] and os.path.isdir(options['--pAplus']):
pAplus_dir = os.path.abspath(options['--pAplus'])
elif options['--pAplus'] and os.path.isfile(options['--pAplus']):
pAplus_dir = hisat_to_tophat(options['--pAplus'], denovo_dir)
else:
sys.exit('You should offer --pAplus option in --as mode!')
if options['--tophat'] and os.path.isdir(options['--tophat']):
tophat_dir = os.path.abspath(options['--tophat'])
elif options['--tophat'] and os.path.isfile(options['--tophat']):
tophat_dir = hisat_to_tophat(options['--tophat'], denovo_dir)
else:
sys.exit('You should offer p(A)minus dir/file in --as mode!')
if not options['--as-type'] or options['--as-type'] == 'CE':
# extract cassette exons
extract_cassette_exon(denovo_dir, tophat_dir, pAplus_dir,
options['--as'], options['--rpkm'])
if not options['--as-type'] or options['--as-type'] == 'RI':
# extract retained introns
extract_retained_intron(denovo_dir, tophat_dir, pAplus_dir,
options['--as'])
if not options['--as-type'] or options['--as-type'] == 'ASS':
# characterize A5SS and A3SS
parse_splice_site(denovo_dir, tophat_dir, pAplus_dir,
options['--as'])
if options['--abs']:
create_dir(options['--abs'])
analyze_abs(denovo_dir, options['--genome'], options['--abs'])
