def crossmap(source_compressed_gtf):
requests.packages.urllib3.util.ssl_.DEFAULT_CIPHERS += 'HIGH:!DH:!aNULL' # Needed for UCSC
# only download if necessary
if not os.path.exists(os.path.join('data', 'hg38ToHg19.over.chain.gz')):
sys.stdout.write('Downloading UCSC database... ')
sys.stdout.flush()
url = 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz'
try:
p = requests.get(url, verify=False)
with open(os.path.join('data', 'hg38ToHg19.over.chain.gz'),
'wb') as o:
o.write(p.content)
except Exception as e:
print(
'\n\nCannot connect to UCSC FTP site. No internet connection?\n'
)
print(f'Exception: {e}')
quit()
sys.stdout.write('\nMaking a hg19-conveterted GTF file\n')
mapTree, targetChromSizes, sourceChromSizes = read_chain_file(
os.path.join('data', 'hg38ToHg19.over.chain.gz'))
converted_gtf = source_compressed_gtf.replace('.gtf.gz',
'.hg19_converted.gtf')
crossmap_gff_file(mapTree, source_compressed_gtf, converted_gtf)
# Note this file is not sorted!
a = pybedtools.BedTool(converted_gtf)
a.sort().remove_invalid().saveas('tmp.txt')
os.rename('tmp.txt', converted_gtf)
args = parser.parse_args()
if len(sys.argv) == 1:
parser.print_help(sys.stderr)
sys.exit(0)
if len(sys.argv) >= 2:
command = sys.argv[1].lower()
args = parser.parse_args()
if command == 'bed':
chain_file = args.chain
in_file = args.in_bed
out_file = args.out_bed
(mapTree, targetChromSizes,
sourceChromSizes) = read_chain_file(chain_file)
crossmap_bed_file(mapTree,
in_file,
out_file,
unmapfile=args.unmap_file,
cstyle=args.cstyle)
elif command == 'bam':
chain_file = args.chain
in_file = args.in_bam
out_file = args.out_bam
if out_file in ["STDOUT", "-"]:
out_file = None
print(args.add_tags)
print("Insert size = %f" % (args.insert_size), file=sys.stderr)
print("Insert size stdev = %f" % (args.insert_size_stdev),
def process_data(options, genome_build):
# Dictionary of Gene objects
genesdata = dict()
# Load custom transcript IDs
transIDs = None
if options.input is not None:
transIDs = readTranscriptIDs(options.input)
print('\nOnly ' + str(len(transIDs)) + ' transcripts read from ' +
options.input + ' are considered\n')
else:
print('\nAll transcripts from the Ensembl release are considered\n')
# Load candidate and CCDS data for Ensembl <75
candidates = dict()
if int(options.ensembl) < 75:
datadir = os.path.dirname(os.path.realpath(__file__)) + '/data'
for line in open(datadir + '/info' + options.ensembl + '.txt'):
line = line.strip()
if line == '': continue
cols = line.split('\t')
if cols[0] not in list(candidates.keys()):
candidates[cols[0]] = dict()
candidates[cols[0]][cols[1]] = int(cols[2])
######################################################################
# Download Ensembl data if necessary
source_compressed_gtf = 'Homo_sapiens.' + genome_build + '.' + options.ensembl + '.gtf.gz'
source_compressed_gtf = os.path.join('data', source_compressed_gtf)
if not os.path.exists(source_compressed_gtf):
sys.stdout.write('Downloading Ensembl database... ')
sys.stdout.flush()
url = 'ftp://ftp.ensembl.org/pub/release-' + options.ensembl + '/gtf/homo_sapiens/Homo_sapiens.' + genome_build + '.' + options.ensembl + '.gtf.gz'
try:
wget.download(url)
os.rename(
'Homo_sapiens.' + genome_build + '.' + options.ensembl +
'.gtf.gz', source_compressed_gtf)
except Exception as e:
print(
'\n\nCannot connect to Ensembl FTP site. No internet connection?\n'
)
print(f'{e}\n{url}')
quit()
################################################################
# Use crossmap to get hg19 if desired
#################################################################
if options.no_hg19 is not False:
requests.packages.urllib3.util.ssl_.DEFAULT_CIPHERS += 'HIGH:!DH:!aNULL' # Needed for UCSC
# only download if necessary
if not os.path.exists(os.path.join('data',
'hg38ToHg19.over.chain.gz')):
sys.stdout.write('Downloading UCSC database... ')
sys.stdout.flush()
url = 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz'
try:
p = requests.get(url, verify=False)
with open(os.path.join('data', 'hg38ToHg19.over.chain.gz'),
'wb') as o:
o.write(p.content)
except Exception as e:
print(
'\n\nCannot connect to UCSC FTP site. No internet connection?\n'
)
print(f'Exception: {e}')
quit()
sys.stdout.write('\nMaking a hg19-conveterted GTF file\n')
mapTree, targetChromSizes, sourceChromSizes = read_chain_file(
os.path.join('data', 'hg38ToHg19.over.chain.gz'))
converted_gtf = os.path.join(
'data', 'Homo_sapiens.hg19_converted' + options.ensembl + '.gtf')
crossmap_gff_file(mapTree, source_compressed_gtf, converted_gtf)
# Note this file is not sorted!
a = pybedtools.BedTool(converted_gtf)
a.sort().remove_invalid().saveas('tmp.txt')
os.rename('tmp.txt', converted_gtf)
################################################################
#
#################################################################
# Iterate through the lines in the ensembl data file
sys.stdout.write('Extracting transcript data from Ensembl...')
transcript, prevenst, first, genesdata = parse_GTF(
filename=source_compressed_gtf,
options=options,
genesdata=genesdata,
transIDs=transIDs)
sys.stdout.write('Done\n')
sys.stdout.flush()
# Finalize last transcript and add to Gene object if candidate
if transcript is not None:
transcript.finalize()
if transcript.isCandidate():
if transcript.ENSG not in list(genesdata.keys()):
genesdata[transcript.ENSG] = Gene(transcript.GENE,
transcript.ENSG)
genesdata[transcript.ENSG].TRANSCRIPTS[
transcript.ENST] = transcript
# If no transcript ID from the input file was found in the Ensembl release
if len(genesdata) == 0:
print('\n\nNo transcripts from ' + options.input +
' found in Ensembl release.')
print('\nNo transcript database created.')
print(
"-----------------------------------------------------------------\n"
)
quit()
write_temp(os.path.join(options.output_dir, options.output + '.txt'),
options, transIDs, genesdata)
enst_records = sort_tmpfile('temp.txt')
assert (len(enst_records) > 0)
writeToFile(enst_records, os.path.join(options.output_dir, options.output))
failed_conversions['GENE'] = set()
failed_conversions['GENETYPE'] = set()
failed_conversions['TRANSTYPE'] = set()
failed_conversions['ENST'] = set()
# ################################################################
# Begin converted GTF conversion
# ################################################################
hg19_records = []
if options.no_hg19 is not False:
sys.stdout.write('Extracting transcript data for hg19 version...')
sys.stdout.flush()
transcript, prevenst, first, genesdata = parse_GTF(
filename=converted_gtf,
options=options,
genesdata=genesdata,
transIDs=transIDs)
# Finalize last transcript and add to Gene object if candidate
if transcript is not None:
try:
transcript.finalize()
except:
warn(transcript)
if transcript.isCandidate():
if transcript.ENSG not in list(genesdata.keys()):
genesdata[transcript.ENSG] = Gene(transcript.GENE,
transcript.ENSG)
genesdata[transcript.ENSG].TRANSCRIPTS[
transcript.ENST] = transcript
# If no transcript ID from the input file was found in the Ensembl release
if len(genesdata) == 0:
print('\n\nNo transcripts from ' + options.input +
' found in Ensembl release.')
print('\nNo transcript database created.')
print(
"-----------------------------------------------------------------\n"
)
quit()
write_temp(
os.path.join(options.output_dir,
options.output + '.hg19_converted.txt'), options,
transIDs, genesdata)
sortedRecords = sort_tmpfile('temp.txt')
writeToFile(
sortedRecords,
os.path.join(options.output_dir,
options.output + '.hg19_converted'))
sys.stdout.write('Completed hg19 version...')
sys.stdout.flush()
pickle.dump(
failed_conversions,
open(
os.path.join(options.output_dir,
options.output + '_failed_conversions.pkl'),
'wb'))
hg19_records = sortedRecords
# ################################################################
# END converted GTF conversion
# ################################################################
# Remove temporary files
sys.stdout.write('OK\n')
sys.stdout.write('Removing temporary files... ')
sys.stdout.flush()
os.remove('temp.txt')
# os.remove(source_compressed_gtf)
print(
f"Failed {failed_conversions['GENE'].__len__()} Genes and {failed_conversions['ENST'].__len__()} transcripts"
)
# Return sorted records
return len(enst_records), len(hg19_records)
args = parser.parse_args()
if len(sys.argv)==1:
parser.print_help(sys.stderr)
sys.exit(0)
if len(sys.argv) >= 2:
command = sys.argv[1].lower()
args = parser.parse_args()
if command == 'bed':
chain_file = args.chain
in_file = args.in_bed
out_file = args.out_bed
(mapTree, targetChromSizes, sourceChromSizes) = read_chain_file(chain_file)
crossmap_bed_file(mapTree, in_file, out_file, unmapfile = args.unmap_file, cstyle = args.cstyle)
elif command == 'bam':
chain_file = args.chain
in_file = args.in_bam
out_file = args.out_bam
if out_file in ["STDOUT","-"]:
out_file = None
print (args.add_tags)
print("Insert size = %f" % (args.insert_size), file=sys.stderr)
print("Insert size stdev = %f" % (args.insert_size_stdev), file=sys.stderr)
print("Number of stdev from the mean = %f" % (args.insert_size_fold), file=sys.stderr)
if args.add_tags:
print("Add tags to each alignment = %s" % (args.add_tags), file=sys.stderr)
}
kwds = list(commands.keys())
if len(sys.argv) == 1:
general_help(commands)
sys.exit(0)
elif len(sys.argv) >= 2:
# deal with bed input
if sys.argv[1].lower() == 'bed':
if len(sys.argv) == 4:
chain_file = sys.argv[2]
in_file = sys.argv[3]
out_file = None
(mapTree, targetChromSizes,
sourceChromSizes) = read_chain_file(chain_file,
print_table=False)
crossmap_bed_file(mapTree, in_file, out_file)
elif len(sys.argv) == 5:
chain_file = sys.argv[2]
in_file = sys.argv[3]
out_file = sys.argv[4]
(mapTree, targetChromSizes,
sourceChromSizes) = read_chain_file(chain_file)
crossmap_bed_file(mapTree, in_file, out_file)
else:
bed_help()
sys.exit(0)
elif sys.argv[1].lower() == 'region':
usage = (
"\nCrossMap.py region <chain_file> <regions.bed> [output_file] [options]\n\nExamples:\nCrossMap.py "
def process_data(options):
# Dictionary of Gene objects
genesdata = dict()
# Load custom transcript IDs
transIDs = None
if options.input is not None:
transIDs = readTranscriptIDs(options.input)
print('\nOnly ' + str(len(transIDs)) + ' transcripts read from ' + options.input + ' are considered\n')
else:
nm = 'All transcripts from the release are considered'
if options.nm_only: nm = 'All NM transcripts from the release are considered'
print(f'\n{nm}\n')
# Load candidate and CCDS data for Ensembl <75
dict()
######################################################################
# Download RefSeq data if necessary
source_compressed_gtf = options.refseq + '_genomic.gtf.gz'
# https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/reference/GCF_000001405.39_GRCh38.p13/GCF_000001405.39_GRCh38.p13_genomic.gtf.gz
source_compressed_gtf = os.path.join('data', source_compressed_gtf)
if not os.path.exists(source_compressed_gtf):
sys.stdout.write('Downloading RefSeq database... ')
sys.stdout.flush()
url = 'https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/reference/' + options.refseq + '/' + options.refseq + '_genomic.gtf.gz'
try:
wget.download(url)
sys.stdout.flush()
# Convert chromosome names #Note we will lose unmapped transcripts here!
print(f'\nUnzipping {options.refseq + "_genomic.gtf.gz"}')
cmd = 'bgzip -d ' + options.refseq + '_genomic.gtf.gz'
os.system(cmd)
out = open('temp.txt', 'w')
print(f'Parsing {options.refseq + "_genomic.gtf"}')
with open(options.refseq + '_genomic.gtf', 'r') as g:
for line in g:
if line.startswith('#'): continue
try:
new_line = replace_chrom_names(line)
except:
print(f'Failed: {line}')
exit()
if new_line:
out.write(new_line)
out.close()
print(f'Compressing the GTF into: {source_compressed_gtf}')
cmd = 'bgzip -c temp.txt > ' + source_compressed_gtf
os.system(cmd)
os.remove('temp.txt')
except Exception as e:
print('\n\nCannot connect to RefSeq FTP site. No internet connection?\n')
print(f'{e}\n{url}')
quit()
################################################################
# Use crossmap to get hg19 if desired
#################################################################
if options.no_hg19 is not False:
requests.packages.urllib3.util.ssl_.DEFAULT_CIPHERS += 'HIGH:!DH:!aNULL' # Needed for UCSC
# only download if necessary
if not os.path.exists(os.path.join('data', 'hg38ToHg19.over.chain.gz')):
sys.stdout.write('Downloading UCSC database... ')
sys.stdout.flush()
url = 'https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz'
try:
p = requests.get(url, verify=False)
with open(os.path.join('data', 'hg38ToHg19.over.chain.gz'), 'wb') as o:
o.write(p.content)
except Exception as e:
print('\n\nCannot connect to UCSC FTP site. No internet connection?\n')
print(f'Exception: {e}')
quit()
converted_gtf = os.path.join('data', 'Homo_sapiens.RefSeq.hg19_converted.' + options.refseq + '.gtf')
if not os.path.exists(converted_gtf):
sys.stdout.write('\nMaking a hg19-conveterted GTF file\n')
mapTree, targetChromSizes, sourceChromSizes = read_chain_file(
os.path.join('data', 'hg38ToHg19.over.chain.gz'))
crossmap_gff_file(mapTree, source_compressed_gtf, converted_gtf)
# Note this file is not sorted!
a = pybedtools.BedTool(converted_gtf)
a.sort().remove_invalid().saveas('tmp.txt')
os.rename('tmp.txt', converted_gtf)
################################################################
#
#################################################################
# Iterate through the lines in the refseq data file
sys.stdout.write('Extracting transcript data from RefSeq...')
transcript, prevenst, first, genesdata = parse_GTF(filename=source_compressed_gtf,
options=options,
genesdata=genesdata,
transIDs=transIDs)
sys.stdout.write('Done\n')
sys.stdout.flush()
# Finalize last transcript and add to Gene object if candidate
if transcript is not None:
transcript.finalize()
if transcript.isCandidate():
if transcript.ENSG not in list(genesdata.keys()): genesdata[transcript.ENSG] = Gene(transcript.GENE,
transcript.ENSG)
genesdata[transcript.ENSG].TRANSCRIPTS[transcript.ENST] = transcript
# If no transcript ID from the input file was found in the Ensembl release
if len(genesdata) == 0:
print('\n\nNo transcripts found in this release.')
print('\nNo transcript database created.')
print("-----------------------------------------------------------------\n")
quit()
write_temp(os.path.join(options.output_dir, options.output + '.txt'), options, transIDs, genesdata)
enst_records = sort_tmpfile('temp.txt')
assert (len(enst_records) > 0)
writeToFile(enst_records, os.path.join(options.output_dir, options.output))
failed_conversions['GENE'] = set()
failed_conversions['GENETYPE'] = set()
failed_conversions['TRANSTYPE'] = set()
failed_conversions['ENST'] = set()
# ################################################################
# Begin converted GTF conversion
# ################################################################
hg19_records = []
if options.no_hg19 is not False:
sys.stdout.write('Extracting transcript data for hg19 version...')
sys.stdout.flush()
transcript, prevenst, first, genesdata = parse_GTF(filename=converted_gtf,
options=options,
genesdata=genesdata,
transIDs=transIDs)
# Finalize last transcript and add to Gene object if candidate
if transcript is not None:
try:
transcript.finalize()
except:
warn(transcript)
if transcript.isCandidate():
if transcript.ENSG not in list(genesdata.keys()): genesdata[transcript.ENSG] = Gene(transcript.GENE,
transcript.ENSG)
genesdata[transcript.ENSG].TRANSCRIPTS[transcript.ENST] = transcript
# If no transcript ID from the input file was found in the release
if len(genesdata) == 0:
print('\n\nNo transcripts from ' + options.input + ' found in the release.')
print('\nNo transcript database created.')
print("-----------------------------------------------------------------\n")
quit()
write_temp(os.path.join(options.output_dir, options.output + '.hg19_converted.txt'), options, transIDs,
genesdata)
sortedRecords = sort_tmpfile('temp.txt')
writeToFile(sortedRecords, os.path.join(options.output_dir, options.output + '.hg19_converted'))
sys.stdout.write('Completed hg19 version...')
sys.stdout.flush()
pickle.dump(failed_conversions,
open(os.path.join(options.output_dir, options.output + '_failed_conversions.pkl'), 'wb'))
hg19_records = sortedRecords
# ################################################################
# END converted GTF conversion
# ################################################################
# Remove temporary files
sys.stdout.write('OK\n')
sys.stdout.write('Removing temporary files... ')
sys.stdout.flush()
os.remove('temp.txt')
os.remove(source_compressed_gtf)
print(f"Failed {failed_conversions['GENE'].__len__()} Genes and {failed_conversions['ENST'].__len__()} transcripts")
# Return sorted records
return len(enst_records), len(hg19_records)