def contigs(args):
step_list = []
(contigs_fasta, database_folder, taxonomy_folder, r, one_minus_r, f,
out_prefix, predicted_proteins_fasta, diamond_file, path_to_prodigal,
path_to_diamond, no_stars, force, quiet, no_log, nproc, sensitive,
block_size, index_chunks, tmpdir, top) = check.convert_arguments(args)
if no_log:
log_file = None
else:
# Check out_prefix already as the log file needs to be written to a
# valid location.
error = check.check_out_prefix(out_prefix, None, quiet)
if error:
sys.exit(1)
log_file = '{0}.log'.format(out_prefix)
with open(log_file, 'w') as outf1:
pass
message = '# CAT v{0}.'.format(about.__version__)
shared.give_user_feedback(message, log_file, quiet, show_time=False)
# Check at which state to start.
if predicted_proteins_fasta is None and diamond_file is None:
message = ('\n'
'CAT is running. Protein prediction, alignment, and contig '
'classification are carried out.\n'
'Rarw!\n\n'
'Supplied command: {0}\n\n'
'Contigs fasta: {1}\n'
'Taxonomy folder: {2}/\n'
'Database folder: {3}/\n'
'Parameter r: {4}\n'
'Parameter f: {5}\n'
'Log file: {6}\n\n'
'-----------------\n'.format(' '.join(sys.argv),
contigs_fasta, taxonomy_folder,
database_folder, args.r,
args.f, log_file))
shared.give_user_feedback(message, log_file, quiet, show_time=False)
step_list.append('run_prodigal')
step_list.append('run_diamond')
elif (predicted_proteins_fasta is not None and diamond_file is None):
message = ('\n'
'CAT is running. Since a predicted protein fasta is '
'supplied, only alignment and contig classification are '
'carried out.\n'
'Rarw!\n\n'
'Supplied command: {0}\n\n'
'Contigs fasta: {1}\n'
'Taxonomy folder: {2}/\n'
'Database folder: {3}/\n'
'Parameter r: {4}\n'
'Parameter f: {5}\n'
'Log file: {6}\n\n'
'-----------------\n'.format(' '.join(sys.argv),
contigs_fasta, taxonomy_folder,
database_folder, args.r,
args.f, log_file))
shared.give_user_feedback(message, log_file, quiet, show_time=False)
step_list.append('run_diamond')
elif (predicted_proteins_fasta is not None and diamond_file is not None):
message = ('\n'
'CAT is running. Since a predicted protein fasta and '
'DIAMOND alignment file are supplied, only contig '
'classification is carried out.\n'
'Rarw!\n\n'
'Supplied command: {0}\n\n'
'Contigs fasta: {1}\n'
'Taxonomy folder: {2}/\n'
'Database folder: {3}/\n'
'Parameter r: {4}\n'
'Parameter f: {5}\n'
'Log file: {6}\n\n'
'-----------------\n'.format(' '.join(sys.argv),
contigs_fasta, taxonomy_folder,
database_folder, args.r,
args.f, log_file))
shared.give_user_feedback(message, log_file, quiet, show_time=False)
elif (predicted_proteins_fasta is None and diamond_file is not None):
message = ('ERROR: if you want CAT to directly do the classification, '
'you should not only supply a DIAMOND alignment table but '
'also a predicted protein fasta file with argument '
'[-p / --proteins].')
shared.give_user_feedback(message, log_file, quiet, error=True)
sys.exit(1)
# Check binaries, output files, taxonomy folder and database folder, and
# set parameters.
message = 'Doing some pre-flight checks first.'
shared.give_user_feedback(message, log_file, quiet, show_time=False)
errors = []
errors.append(check.check_out_prefix(out_prefix, log_file, quiet))
if 'run_prodigal' in step_list:
errors.append(
check.check_prodigal_binaries(path_to_prodigal, log_file, quiet))
predicted_proteins_fasta = ('{0}.predicted_proteins.faa'
''.format(out_prefix))
predicted_proteins_gff = ('{0}.predicted_proteins.gff'
''.format(out_prefix))
if not force:
errors.append(
check.check_output_file(predicted_proteins_fasta, log_file,
quiet))
errors.append(
check.check_output_file(predicted_proteins_gff, log_file,
quiet))
if 'run_diamond' in step_list:
errors.append(
check.check_diamond_binaries(path_to_diamond, log_file, quiet))
diamond_file = '{0}.alignment.diamond'.format(out_prefix)
if not force:
errors.append(
check.check_output_file(diamond_file, log_file, quiet))
else:
diamond_file = diamond_file
errors.append(
check.check_folders_for_run(taxonomy_folder, database_folder,
step_list, log_file, quiet))
contig2classification_output_file = ('{0}.contig2classification.txt'
''.format(out_prefix))
ORF2LCA_output_file = '{0}.ORF2LCA.txt'.format(out_prefix)
if not force:
errors.append(
check.check_output_file(contig2classification_output_file,
log_file, quiet))
errors.append(
check.check_output_file(ORF2LCA_output_file, log_file, quiet))
if 'run_prodigal' not in step_list:
if not check.check_whether_file_is_fasta(predicted_proteins_fasta):
message = ('ERROR: {0} is not a fasta file.'
''.format(predicted_proteins_fasta))
shared.give_user_feedback(message, log_file, quiet, error=True)
errors.append(True)
errors.append(check.check_top(top, r, log_file, quiet))
if True in errors:
sys.exit(1)
(nodes_dmp, names_dmp, prot_accession2taxid_file
) = check.inspect_taxonomy_folder(taxonomy_folder)
(nr_file, diamond_database, fastaid2LCAtaxid_file,
taxids_with_multiple_offspring_file
) = check.inspect_database_folder(database_folder)
message = 'Ready to fly!\n\n-----------------\n'
shared.give_user_feedback(message, log_file, quiet, show_time=False)
# Start CAT.
contig_names = shared.import_contig_names(contigs_fasta, log_file, quiet)
if 'run_prodigal' in step_list:
shared.run_prodigal(path_to_prodigal, contigs_fasta,
predicted_proteins_fasta, predicted_proteins_gff,
log_file, quiet)
contig2ORFs = shared.import_ORFs(predicted_proteins_fasta, log_file, quiet)
check.check_whether_ORFs_are_based_on_contigs(contig_names, contig2ORFs,
log_file, quiet)
if 'run_diamond' in step_list:
shared.run_diamond(path_to_diamond, diamond_database,
predicted_proteins_fasta, diamond_file, nproc,
sensitive, block_size, index_chunks, tmpdir, top,
log_file, quiet)
(ORF2hits, all_hits) = shared.parse_diamond_file(diamond_file, one_minus_r,
log_file, quiet)
(taxid2parent, taxid2rank) = tax.import_nodes(nodes_dmp, log_file, quiet)
fastaid2LCAtaxid = tax.import_fastaid2LCAtaxid(fastaid2LCAtaxid_file,
all_hits, log_file, quiet)
taxids_with_multiple_offspring = tax.import_taxids_with_multiple_offspring(
taxids_with_multiple_offspring_file, log_file, quiet)
message = ('CAT is spinning! Files {0} and {1} are created.'
''.format(contig2classification_output_file,
ORF2LCA_output_file))
shared.give_user_feedback(message, log_file, quiet)
number_of_classified_contigs = 0
with open(contig2classification_output_file,
'w') as outf1, open(ORF2LCA_output_file, 'w') as outf2:
outf1.write('# contig\tclassification\treason\tlineage\t'
'lineage scores\n')
outf2.write('# ORF\tlineage\tbit-score\n')
for contig in sorted(contig_names):
if contig not in contig2ORFs:
outf1.write('{0}\tunclassified\tno ORFs found\n'
''.format(contig))
continue
LCAs_ORFs = []
for ORF in contig2ORFs[contig]:
if ORF not in ORF2hits:
outf2.write('{0}\tORF has no hit to database\n'
''.format(ORF))
continue
(taxid,
top_bitscore) = tax.find_LCA_for_ORF(ORF2hits[ORF],
fastaid2LCAtaxid,
taxid2parent)
if taxid.startswith('no taxid found'):
outf2.write('{0}\t{1}\t{2}\n'.format(
ORF, taxid, top_bitscore))
else:
lineage = tax.find_lineage(taxid, taxid2parent)
if not no_stars:
lineage = tax.star_lineage(
lineage, taxids_with_multiple_offspring)
outf2.write('{0}\t{1}\t{2}\n'
''.format(ORF, ';'.join(lineage[::-1]),
top_bitscore))
LCAs_ORFs.append((taxid, top_bitscore), )
if len(LCAs_ORFs) == 0:
outf1.write('{0}\tunclassified\tno hits to database\n'
''.format(contig))
continue
(lineages, lineages_scores,
based_on_number_of_ORFs) = tax.find_weighted_LCA(
LCAs_ORFs, taxid2parent, f)
if lineages == 'no ORFs with taxids found.':
outf1.write('{0}\tunclassified\t'
'hits not found in taxonomy files\n'
''.format(contig))
continue
if lineages == 'no lineage whitelisted.':
outf1.write('{0}\tunclassified\t'
'no lineage reached minimum bit-score support\n'
''.format(contig))
continue
# The contig has a valid classification.
number_of_classified_contigs += 1
for (i, lineage) in enumerate(lineages):
if not no_stars:
lineage = tax.star_lineage(lineage,
taxids_with_multiple_offspring)
scores = [
'{0:.2f}'.format(score) for score in lineages_scores[i]
]
if len(lineages) == 1:
# There is only one classification.
outf1.write('{0}\tclassified\t'
'based on {1}/{2} ORFs\t{3}\t{4}\n'
''.format(contig, based_on_number_of_ORFs,
len(contig2ORFs[contig]),
';'.join(lineage[::-1]),
';'.join(scores[::-1])))
else:
# There are multiple classifications.
outf1.write('{0}\tclassified ({1}/{2})\t'
'based on {3}/{4} ORFs\t{5}\t{6}\n'
''.format(contig, i + 1, len(lineages),
based_on_number_of_ORFs,
len(contig2ORFs[contig]),
';'.join(lineage[::-1]),
';'.join(scores[::-1])))
message = ('\n-----------------\n\n'
'[{0}] CAT is done! {1}/{2} contigs classified.'
''.format(datetime.datetime.now(), number_of_classified_contigs,
len(contig_names)))
shared.give_user_feedback(message, log_file, quiet, show_time=False)
if f < 0.5:
message = ('\nWARNING: since f is set to smaller than 0.5, one '
'contig may have multiple classifications.')
shared.give_user_feedback(message, log_file, quiet, show_time=False)
def run_existing(args, date):
step_list = []
(database_folder,
taxonomy_folder,
path_to_diamond,
quiet,
no_log,
nproc) = check.convert_arguments(args)
if no_log:
log_file = None
else:
log_file = '{0}.CAT_prepare.existing.log'.format(date)
with open(log_file, 'w') as outf1:
pass
message = '# CAT v{0}.'.format(about.__version__)
shared.give_user_feedback(message, log_file, quiet, show_time=False)
message = ('\n'
'CAT prepare is running, constructing only parts of the '
'database that are missing. Rawr!\n\n'
'WARNING: CAT prepare at this point does not check whether the '
'existing files are OK or corrupted, only if they are there.\n'
'WARNING: note that the database and taxonomy files should be '
'downloaded preferably at the same date.\n'
'WARNING: preparing the database files may take a couple of '
'hours.\n\n'
'Supplied command: {0}\n\n'
'Supplied command: {0}\n\n'
'Taxonomy folder: {1}/\n'
'Database folder: {2}/\n'
'Log file: {3}\n\n'
'-----------------\n'.format(' '.join(sys.argv),
taxonomy_folder,
database_folder,
log_file))
shared.give_user_feedback(message, log_file, quiet, show_time=False)
message = 'Doing some pre-flight checks first.'
shared.give_user_feedback(message, log_file, quiet, show_time=False)
# Check DIAMOND path.
error = check.check_diamond_binaries(path_to_diamond, log_file, quiet)
if error:
sys.exit(1)
# Check taxonomy folder.
taxonomy_folder_inspect = check.inspect_taxonomy_folder(taxonomy_folder)
if taxonomy_folder_inspect == [None]:
message = ('Taxonomy folder not found. Directory will be created '
'fresh and taxonomy files downloaded to it.')
shared.give_user_feedback(message, log_file, quiet)
nodes_dmp = None
names_dmp = None
prot_accession2taxid_file = None
else:
(nodes_dmp,
names_dmp,
prot_accession2taxid_file) = taxonomy_folder_inspect
message = ('Taxonomy folder found.')
shared.give_user_feedback(message, log_file, quiet)
if ((nodes_dmp is None and names_dmp is not None) or
(nodes_dmp is not None and names_dmp is None)):
message = ('ERROR: CAT prepare did not find both nodes.dmp and '
'names.dmp in the taxonomy folder. They should be '
'downloaded together. Remove {0} and try again.'
''.format([file_ for file_ in (nodes_dmp, names_dmp) if
file_ is not None][0]))
shared.give_user_feedback(message, log_file, quiet, error=True)
sys.exit(1)
if nodes_dmp is None and names_dmp is None:
message = ('Nodes.dmp and names.dmp will be downloaded to taxonomy '
'folder.')
shared.give_user_feedback(message, log_file, quiet)
step_list.append('download_taxonomy_files')
else:
message = 'Nodes.dmp found: {0}.'.format(nodes_dmp)
shared.give_user_feedback(message, log_file, quiet)
message = 'Names.dmp found: {0}.'.format(names_dmp)
shared.give_user_feedback(message, log_file, quiet)
if prot_accession2taxid_file is None:
message = ('Prot.accession2taxid file will be downloaded to taxonomy '
'folder.')
shared.give_user_feedback(message, log_file, quiet)
prot_accession2taxid_file = ('{0}/{1}.prot.accession2taxid.gz'
''.format(taxonomy_folder, date))
step_list.append('download_prot_accession2taxid_file')
else:
message = ('Prot.accession2taxid file found: {0}.'
''.format(prot_accession2taxid_file))
shared.give_user_feedback(message, log_file, quiet)
# Check database folder.
database_folder_inspect = check.inspect_database_folder(database_folder)
if database_folder_inspect == [None]:
message = ('Database folder not found. Directory will be created '
'fresh and necessary database files will be downloaded to '
'it / constructed in it.')
shared.give_user_feedback(message, log_file, quiet)
nr_file = None
diamond_database = None
fastaid2LCAtaxid_file = None
taxids_with_multiple_offspring_file = None
else:
(nr_file,
diamond_database,
fastaid2LCAtaxid_file,
taxids_with_multiple_offspring_file) = database_folder_inspect
message = ('Database folder found.')
shared.give_user_feedback(message, log_file, quiet)
tmp = (diamond_database,
fastaid2LCAtaxid_file,
taxids_with_multiple_offspring_file)
if (nr_file is None and
None in tmp and
not all([file_ is None for file_ in tmp])):
message = ('ERROR: Database folder does not contain an nr file, while '
'some but not all of the downstream files that depend on '
'it are present. In order to prevent strange bugs from '
'arising, please remove all files from the database folder '
'and try again.')
shared.give_user_feedback(message, log_file, quiet, error=True)
sys.exit(1)
if (fastaid2LCAtaxid_file is None and
taxids_with_multiple_offspring_file is not None):
message = ('ERROR: file taxids_with_multiple_offspring exists but '
'fastaid2LCAtaxid is not found in the database folder '
'whilst taxids_with_multiple_offspring depends on it. In '
'order to prevent strange bugs from arising, please remove '
'{0} and try again.'
''.format(taxids_with_multiple_offspring_file))
shared.give_user_feedback(message, log_file, quiet, error=True)
sys.exit(1)
whether_to_download_nr = True
if (nr_file is None and
diamond_database is not None and
fastaid2LCAtaxid_file is not None and
taxids_with_multiple_offspring_file is not None):
whether_to_download_nr = False
if nr_file is None:
if whether_to_download_nr:
message = 'Nr file will be downloaded to database folder.'
shared.give_user_feedback(message, log_file, quiet)
nr_file = '{0}/{1}.nr.gz'.format(database_folder, date)
step_list.append('download_nr')
else:
pass
else:
message = 'Nr file found: {0}.'.format(nr_file)
shared.give_user_feedback(message, log_file, quiet)
if diamond_database is None:
message = ('DIAMOND database will be constructed from the nr file.'
''.format(nr_file))
shared.give_user_feedback(message, log_file, quiet)
diamond_database_prefix = '{0}/{1}.nr'.format(database_folder, date)
step_list.append('make_diamond_database')
else:
message = 'DIAMOND database found: {0}.'.format(diamond_database)
shared.give_user_feedback(message, log_file, quiet)
diamond_database_prefix = diamond_database.rsplit('.dmnd', 1)[0]
if fastaid2LCAtaxid_file is None:
message = 'File fastaid2LCAtaxid will be created.'
shared.give_user_feedback(message, log_file, quiet)
fastaid2LCAtaxid_file = ('{0}/{1}.nr.fastaid2LCAtaxid'
''.format(database_folder, date))
step_list.append('make_fastaid2LCAtaxid_file')
else:
message = ('Fastaid2LCAtaxid found: {0}.'
''.format(fastaid2LCAtaxid_file))
shared.give_user_feedback(message, log_file, quiet)
if taxids_with_multiple_offspring_file is None:
message = 'File taxids_with_multiple_offspring will be created.'
shared.give_user_feedback(message, log_file, quiet)
taxids_with_multiple_offspring_file = ('{0}/{1}.nr.taxids_with_'
'multiple_offspring'
''.format(database_folder,
date))
step_list.append('make_taxids_with_multiple_offspring_file')
else:
message = ('Taxids_with_multiple_offspring found: {0}.'
''.format(taxids_with_multiple_offspring_file))
shared.give_user_feedback(message, log_file, quiet)
if nr_file is None and whether_to_download_nr is False:
# This is pushed here just for the logic of the user.
message = ('NOTE: Database folder contains all the necessary files '
'except for nr.gz. Since nr.gz is not used by CAT or BAT, '
'this is fine.')
shared.give_user_feedback(message, log_file, quiet)
if taxonomy_folder_inspect == [None] and database_folder_inspect == [None]:
message = ('\n-----------------\n\n'
'WARNING: no taxonomy or database folder was found. CAT '
'prepare will create them fresh. Are you sure you are '
'linking to existing folders?')
shared.give_user_feedback(message, log_file, quiet, show_time=False)
if ('make_fastaid2LCAtaxid_file' in step_list or
'make_taxids_with_multiple_offspring_file' in step_list):
# Check memory.
min_mem = 100
(total_memory, error) = check.check_memory(min_mem)
if error:
message = ('ERROR: at least {0}GB of memory is needed for the '
'database construction. {1}GB is found on your system. '
'You can either try to find a machine with more '
'memory, or download preconstructed database files '
'from tbb.bio.uu.nl/bastiaan/CAT_prepare/.'
''.format(min_mem, total_memory))
shared.give_user_feedback(message, log_file, quiet, error=True)
sys.exit(1)
if len(step_list) == 0:
message = ('All necessary files are found. Existing database does not '
'need any more work...')
shared.give_user_feedback(message, log_file, quiet, show_time=False)
else:
message = 'Ready to fly!\n\n-----------------\n'
shared.give_user_feedback(message, log_file, quiet, show_time=False)
if taxonomy_folder_inspect == [None]:
os.mkdir(taxonomy_folder)
message = 'Taxonomy folder {0} is created.'.format(taxonomy_folder)
shared.give_user_feedback(message, log_file, quiet)
if database_folder_inspect == [None]:
os.mkdir(database_folder)
message = 'Database folder {0} is created.'.format(database_folder)
shared.give_user_feedback(message, log_file, quiet)
prepare(step_list,
taxonomy_folder,
database_folder,
date,
prot_accession2taxid_file,
nr_file,
path_to_diamond,
diamond_database_prefix,
nproc,
fastaid2LCAtaxid_file,
taxids_with_multiple_offspring_file,
log_file,
quiet)
def run_fresh(args, date):
(database_folder,
taxonomy_folder,
path_to_diamond,
quiet,
no_log,
nproc) = check.convert_arguments(args)
if no_log:
log_file = None
else:
log_file = '{0}.CAT_prepare.fresh.log'.format(date)
with open(log_file, 'w') as outf1:
pass
message = '# CAT v{0}.'.format(about.__version__)
shared.give_user_feedback(message, log_file, quiet, show_time=False)
message = ('\n'
'CAT prepare is running, constructing a fresh database.\n'
'Rawr!\n\n'
'WARNING: preparing the database files may take a couple of '
'hours.\n\n'
'Supplied command: {0}\n\n'
'Taxonomy folder: {1}/\n'
'Database folder: {2}/\n'
'Log file: {3}\n\n'
'-----------------\n'.format(' '.join(sys.argv),
taxonomy_folder,
database_folder,
log_file))
shared.give_user_feedback(message, log_file, quiet, show_time=False)
# Check diamond path.
error = check.check_diamond_binaries(path_to_diamond, log_file, quiet)
if error:
sys.exit(1)
# Check taxonomy folder.
taxonomy_folder_inspect = check.inspect_taxonomy_folder(taxonomy_folder)
if taxonomy_folder_inspect != [None]:
if len([file for file in taxonomy_folder_inspect if
file is not None]) > 0:
message = ('ERROR: taxonomy folder {0} exists already and '
'contains taxonomy files. Please supply a novel or '
'empty folder if you want to start fresh, or run '
'CAT prepare --existing.'
''.format(taxonomy_folder))
shared.give_user_feedback(message, log_file, quiet, error=True)
sys.exit(1)
message = ('Taxonomy folder exists already. Taxonomy files will be '
'downloaded to it.')
shared.give_user_feedback(message, log_file, quiet)
database_folder_inspect = check.inspect_database_folder(database_folder)
# Check database folder.
if database_folder_inspect != [None]:
if len([file_ for file_ in database_folder_inspect if
file_ is not None]) > 0:
message = ('ERROR: database folder {0} exists already and '
'contains database files. Please supply a novel or '
'empty folder if you want to start fresh.'
''.format(database_folder))
shared.give_user_feedback(message, log_file, quiet, error=True)
sys.exit(1)
message = ('Database folder exists already. Database file will be '
'downloaded to it / constructed in it.')
shared.give_user_feedback(message, log_file, quiet)
# Check memory.
min_mem = 100
(total_memory, error) = check.check_memory(min_mem)
if error:
message = ('ERROR: at least {0}GB of memory is needed for a fresh '
'database construction. {1}GB is found on your system. You '
'can either try to find a machine with more memory, or '
'download preconstructed database files from '
'tbb.bio.uu.nl/bastiaan/CAT_prepare/.'
''.format(min_mem, total_memory))
shared.give_user_feedback(message, log_file, quiet, error=True)
sys.exit(1)
if taxonomy_folder_inspect == [None]:
os.mkdir(taxonomy_folder)
message = '{0} is created.'.format(taxonomy_folder)
shared.give_user_feedback(message, log_file, quiet)
if database_folder_inspect == [None]:
os.mkdir(database_folder)
message = '{0} is created.'.format(database_folder)
shared.give_user_feedback(message, log_file, quiet)
prot_accession2taxid_file = ('{0}/{1}.prot.accession2taxid.gz'
''.format(taxonomy_folder, date))
nr_file = '{0}/{1}.nr.gz'.format(database_folder, date)
diamond_database_prefix = '{0}/{1}.nr'.format(database_folder, date)
fastaid2LCAtaxid_file = ('{0}/{1}.nr.fastaid2LCAtaxid'
''.format(database_folder, date))
taxids_with_multiple_offspring_file = ('{0}/{1}.nr.taxids_with_multiple_'
'offspring'
''.format(database_folder, date))
step_list = ['download_taxonomy_files',
'download_prot_accession2taxid_file',
'download_nr',
'make_diamond_database',
'make_fastaid2LCAtaxid_file',
'make_taxids_with_multiple_offspring_file']
prepare(step_list,
taxonomy_folder,
database_folder,
date,
prot_accession2taxid_file,
nr_file,
path_to_diamond,
diamond_database_prefix,
nproc,
fastaid2LCAtaxid_file,
taxids_with_multiple_offspring_file,
log_file,
quiet)
def run():
args = parse_arguments()
message = '# CAT v{0}.'.format(about.__version__)
shared.give_user_feedback(message, args.log_file, args.quiet,
show_time=False)
# Check at which state to start.
step_list = []
if not args.proteins_fasta and not args.alignment_file:
message = (
'\n'
'BAT is running. Protein prediction, alignment, and bin '
'classification are carried out.')
shared.give_user_feedback(message, args.log_file, args.quiet,
show_time=False)
step_list.append('predict_proteins')
step_list.append('align')
elif args.proteins_fasta and not args.alignment_file:
message = (
'\n'
'BAT is running. Since a predicted protein fasta is supplied, '
'only alignment and bin classification are carried out.')
shared.give_user_feedback(message, args.log_file, args.quiet,
show_time=False)
step_list.append('align')
elif args.proteins_fasta and args.alignment_file:
message = (
'\n'
'BAT is running. Since a predicted protein fasta and '
'alignment file are supplied, only bin classification is '
'carried out.')
shared.give_user_feedback(message, args.log_file, args.quiet,
show_time=False)
elif not args.proteins_fasta and args.alignment_file:
message = (
'if you want BAT to directly classify a set of bins, you '
'should not only supply a DIAMOND alignment table but also a '
'concatenated predicted protein fasta file with argument '
'[-p / --proteins].')
shared.give_user_feedback(message, args.log_file, args.quiet,
error=True)
sys.exit(1)
step_list.append('classify')
# Print variables.
message = (
'Rarw!\n\n'
'Supplied command: {0}\n\n'
'Bin folder: {1}\n'
'Taxonomy folder: {2}\n'
'Database folder: {3}\n'
'Parameter r: {4}\n'
'Parameter f: {5}\n'
'Log file: {6}\n\n'
'-----------------\n'.format(
' '.join(sys.argv),
args.bin_folder,
args.taxonomy_folder,
args.database_folder,
int(args.r),
float(args.f),
args.log_file))
shared.give_user_feedback(message, args.log_file, args.quiet,
show_time=False)
# Check binaries, output files, taxonomy folder and database folder, and
# set variables.
message = 'Doing some pre-flight checks first.'
shared.give_user_feedback(message, args.log_file, args.quiet,
show_time=False)
errors = []
errors.append(
check.check_bin_folder(
args.bin_folder, args.bin_suffix, args.log_file, args.quiet))
errors.append(
check.check_out_prefix(args.out_prefix, args.log_file, args.quiet))
if 'predict_proteins' in step_list:
errors.append(
check.check_prodigal_binaries(
args.path_to_prodigal, args.log_file, args.quiet))
setattr(args,
'concatenated_fasta',
'{0}.concatenated.fasta'.format(args.out_prefix))
setattr(args,
'proteins_fasta',
'{0}.concatenated.predicted_proteins.faa'.format(
args.out_prefix))
setattr(args,
'proteins_gff',
'{0}.concatenated.predicted_proteins.gff'.format(
args.out_prefix))
if not args.force:
errors.append(
check.check_output_file(
args.concatenated_fasta, args.log_file, args.quiet))
errors.append(
check.check_output_file(
args.proteins_fasta, args.log_file, args.quiet))
errors.append(
check.check_output_file(
args.proteins_gff, args.log_file, args.quiet))
if 'align' in step_list:
errors.append(
check.check_diamond_binaries(
args.path_to_diamond, args.log_file, args.quiet))
setattr(args,
'alignment_file',
'{0}.concatenated.alignment.diamond'.format(args.out_prefix))
if not args.force:
errors.append(
check.check_output_file(
args.alignment_file, args.log_file, args.quiet))
errors.append(
check.check_folders_for_run(
args.taxonomy_folder,
args.nodes_dmp,
args.names_dmp,
args.database_folder,
args.diamond_database,
args.fastaid2LCAtaxid_file,
args.taxids_with_multiple_offspring_file,
step_list,
args.log_file,
args.quiet))
setattr(args,
'bin2classification_output_file',
'{0}.bin2classification.txt'.format(args.out_prefix))
setattr(args,
'ORF2LCA_output_file',
'{0}.ORF2LCA.txt'.format(args.out_prefix))
if not args.force:
errors.append(
check.check_output_file(
args.bin2classification_output_file,
args.log_file,
args.quiet))
errors.append(
check.check_output_file(
args.ORF2LCA_output_file, args.log_file, args.quiet))
if 'predict_proteins' not in step_list:
errors.append(
check.check_fasta(
args.proteins_fasta, args.log_file, args.quiet))
if 'align' in step_list:
errors.append(
check.check_top(args.top, args.r, args.log_file, args.quiet))
# Print all variables.
shared.print_variables(args, step_list)
if True in errors:
sys.exit(1)
message = 'Ready to fly!\n\n-----------------\n'
shared.give_user_feedback(message, args.log_file, args.quiet,
show_time=False)
# Start BAT.
(bin2contigs, contig_names) = import_bins(
args.bin_folder, args.bin_suffix, args.log_file, args.quiet)
if 'predict_proteins' in step_list:
make_concatenated_fasta(
args.concatenated_fasta,
bin2contigs,
args.bin_folder,
args.log_file,
args.quiet)
shared.run_prodigal(
args.path_to_prodigal,
args.concatenated_fasta,
args.proteins_fasta,
args.proteins_gff,
args.log_file,
args.quiet)
contig2ORFs = shared.import_ORFs(
args.proteins_fasta, args.log_file, args.quiet)
check.check_whether_ORFs_are_based_on_contigs(
contig_names, contig2ORFs, args.log_file, args.quiet)
if 'align' in step_list:
shared.run_diamond(args)
(ORF2hits,
all_hits) = shared.parse_tabular_alignment(
args.alignment_file,
args.one_minus_r,
args.log_file,
args.quiet)
(taxid2parent,
taxid2rank) = tax.import_nodes(
args.nodes_dmp, args.log_file, args.quiet)
fastaid2LCAtaxid = tax.import_fastaid2LCAtaxid(
args.fastaid2LCAtaxid_file, all_hits, args.log_file, args.quiet)
taxids_with_multiple_offspring = tax.import_taxids_with_multiple_offspring(
args.taxids_with_multiple_offspring_file,
args.log_file,
args.quiet)
message = 'BAT is flying! Files {0} and {1} are created.'.format(
args.bin2classification_output_file, args.ORF2LCA_output_file)
shared.give_user_feedback(message, args.log_file, args.quiet)
n_classified_bins = 0
with open(args.bin2classification_output_file, 'w') as outf1, open(args.ORF2LCA_output_file, 'w') as outf2:
outf1.write('# bin\tclassification\treason\tlineage\tlineage scores\n')
outf2.write('# ORF\tbin\tnumber of hits\tlineage\ttop bit-score\n')
for bin_ in sorted(bin2contigs):
LCAs_ORFs = []
for contig in sorted(bin2contigs[bin_]):
if contig not in contig2ORFs:
continue
for ORF in contig2ORFs[contig]:
if ORF not in ORF2hits:
outf2.write('{0}\t{1}\tORF has no hit to database\n'
''.format(ORF, bin_))
continue
n_hits = len(ORF2hits[ORF])
(taxid,
top_bitscore) = tax.find_LCA_for_ORF(
ORF2hits[ORF],
fastaid2LCAtaxid,
taxid2parent)
if taxid.startswith('no taxid found'):
outf2.write('{0}\t{1}\t{2}\t{3}\t{4}\n'.format(
ORF, bin_, n_hits, taxid, top_bitscore))
else:
lineage = tax.find_lineage(taxid, taxid2parent)
if not args.no_stars:
lineage = tax.star_lineage(
lineage, taxids_with_multiple_offspring)
outf2.write('{0}\t{1}\t{2}\t{3}\t{4}\n'.format(
ORF,
bin_,
n_hits,
';'.join(lineage[::-1]),
top_bitscore))
LCAs_ORFs.append((taxid, top_bitscore),)
if len(LCAs_ORFs) == 0:
outf1.write('{0}\tno taxid assigned\tno hits to database\n'
''.format(bin_))
continue
(lineages,
lineages_scores,
based_on_n_ORFs) = tax.find_weighted_LCA(
LCAs_ORFs, taxid2parent, args.f)
if lineages == 'no ORFs with taxids found.':
outf1.write('{0}\tno taxid assigned\t'
'hits not found in taxonomy files\n'.format(bin_))
continue
if lineages == 'no lineage whitelisted.':
outf1.write(
'{0}\tno taxid assigned\t'
'no lineage reached minimum bit-score support\n'
''.format(bin_))
continue
# The bin has a valid classification.
n_classified_bins += 1
total_n_ORFs = sum([len(contig2ORFs[contig]) for
contig in bin2contigs[bin_] if contig in contig2ORFs])
for (i, lineage) in enumerate(lineages):
if not args.no_stars:
lineage = tax.star_lineage(
lineage, taxids_with_multiple_offspring)
scores = ['{0:.2f}'.format(score) for
score in lineages_scores[i]]
if len(lineages) == 1:
# There is only one classification.
outf1.write(
'{0}\t'
'taxid assigned\t'
'based on {1}/{2} ORFs\t'
'{3}\t'
'{4}\n'.format(
bin_,
based_on_n_ORFs,
total_n_ORFs,
';'.join(lineage[::-1]),
';'.join(scores[::-1])))
else:
# There are multiple classifications.
outf1.write(
'{0}\t'
'taxid assigned ({1}/{2})\t'
'based on {3}/{4} ORFs\t'
'{5}\t'
'{6}\n'.format(
bin_,
i + 1,
len(lineages),
based_on_n_ORFs,
total_n_ORFs,
';'.join(lineage[::-1]),
';'.join(scores[::-1])))
message = ('\n-----------------\n\n'
'{0} BAT is done! {1:,d}/{2:,d} bins have taxonomy assigned.'
''.format(shared.timestamp(), n_classified_bins, len(bin2contigs)))
shared.give_user_feedback(message, args.log_file, args.quiet,
show_time=False)
if args.f < 0.5:
message = ('\nWARNING: since f is set to smaller than 0.5, one bin '
'may have multiple classifications.')
shared.give_user_feedback(message, args.log_file, args.quiet,
show_time=False)
return
def run_existing(args):
step_list = []
message = '# CAT v{0}.'.format(about.__version__)
shared.give_user_feedback(message,
args.log_file,
args.quiet,
show_time=False)
message = (
'\n'
'CAT prepare is running, constructing only parts of the database '
'that are missing. Rawr!\n\n'
'WARNING: CAT prepare does not check whether the existing files '
'are OK or corrupted, only if they are there.\n'
'WARNING: note that the database and taxonomy files should be '
'downloaded preferably at the same date.\n'
'WARNING: preparing the database files may take a couple of hours.'
'\n\n'
'Supplied command: {0}\n\n'
'Taxonomy folder: {1}\n'
'Database folder: {2}\n'
'Log file: {3}\n\n'
'-----------------\n'.format(' '.join(sys.argv), args.taxonomy_folder,
args.database_folder, args.log_file))
shared.give_user_feedback(message,
args.log_file,
args.quiet,
show_time=False)
message = 'Doing some pre-flight checks first.'
shared.give_user_feedback(message,
args.log_file,
args.quiet,
show_time=False)
# Check DIAMOND path.
error = check.check_diamond_binaries(args.path_to_diamond, args.log_file,
args.quiet)
if error:
sys.exit(1)
# Check taxonomy folder.
if not os.path.isdir(args.taxonomy_folder):
message = ('Taxonomy folder not found. Directory will be created '
'fresh and taxonomy files downloaded to it.')
shared.give_user_feedback(message, args.log_file, args.quiet)
else:
message = ('Taxonomy folder found.')
shared.give_user_feedback(message, args.log_file, args.quiet)
if ((not args.nodes_dmp and args.names_dmp)
or (args.nodes_dmp and not args.names_dmp)):
message = (
'CAT prepare did not find both nodes.dmp and names.dmp in the '
'taxonomy folder. They should be downloaded together. Remove '
'{0} and try again.'.format([
file_ for file_ in (args.nodes_dmp, args.names_dmp) if file_
][0]))
shared.give_user_feedback(message,
args.log_file,
args.quiet,
error=True)
sys.exit(1)
if not args.nodes_dmp and not args.names_dmp:
message = ('Nodes.dmp and names.dmp will be downloaded to taxonomy '
'folder.')
shared.give_user_feedback(message, args.log_file, args.quiet)
step_list.append('download_taxonomy_files')
else:
message = 'Nodes.dmp found: {0}.'.format(args.nodes_dmp)
shared.give_user_feedback(message, args.log_file, args.quiet)
message = 'Names.dmp found: {0}.'.format(args.names_dmp)
shared.give_user_feedback(message, args.log_file, args.quiet)
if not args.prot_accession2taxid_file:
# NOTE that the file will only be downloaded if a new
# fastaid2LCAtaxid_file needs to be constructed.
message = 'Prot.accession2taxid file not found in taxonomy folder.'
shared.give_user_feedback(message, args.log_file, args.quiet)
else:
message = 'Prot.accession2taxid file found: {0}.'.format(
args.prot_accession2taxid_file)
shared.give_user_feedback(message, args.log_file, args.quiet)
# Check database folder.
if not os.path.isdir(args.database_folder):
message = (
'Database folder not found. Directory will be created fresh '
'and necessary database files will be downloaded to '
'it / constructed in it.')
shared.give_user_feedback(message, args.log_file, args.quiet)
else:
message = ('Database folder found.')
shared.give_user_feedback(message, args.log_file, args.quiet)
tmp = (args.diamond_database, args.fastaid2LCAtaxid_file,
args.taxids_with_multiple_offspring_file)
if (not args.nr_file and None in tmp
and not all([file_ is None for file_ in tmp])):
message = (
'database folder does not contain an nr file, while some but '
'not all of the downstream files that depend on it are '
'present. In order to prevent strange bugs from arising, '
'remove all files from the database folder and try again.')
shared.give_user_feedback(message,
args.log_file,
args.quiet,
error=True)
sys.exit(1)
if (not args.fastaid2LCAtaxid_file
and args.taxids_with_multiple_offspring_file):
message = (
'file taxids_with_multiple_offspring exists but '
'fastaid2LCAtaxid is not found in the database folder whilst '
'taxids_with_multiple_offspring depends on it. In order to '
'prevent strange bugs from arising, remove {0} and try again.'
''.format(args.taxids_with_multiple_offspring_file))
shared.give_user_feedback(message,
args.log_file,
args.quiet,
error=True)
sys.exit(1)
whether_to_download_nr = True
if (not args.nr_file and args.diamond_database
and args.fastaid2LCAtaxid_file
and args.taxids_with_multiple_offspring_file):
whether_to_download_nr = False
if not args.nr_file:
if whether_to_download_nr:
message = 'Nr file will be downloaded to database folder.'
shared.give_user_feedback(message, args.log_file, args.quiet)
step_list.append('download_nr')
else:
pass
else:
message = 'Nr file found: {0}.'.format(args.nr_file)
shared.give_user_feedback(message, args.log_file, args.quiet)
if not args.diamond_database:
message = 'DIAMOND database will be constructed from the nr file.'
shared.give_user_feedback(message, args.log_file, args.quiet)
step_list.append('make_diamond_database')
else:
message = 'DIAMOND database found: {0}.'.format(args.diamond_database)
shared.give_user_feedback(message, args.log_file, args.quiet)
if not args.fastaid2LCAtaxid_file:
if not args.prot_accession2taxid_file:
message = ('Prot.accession2taxid file will be downloaded to '
'taxonomy folder.')
shared.give_user_feedback(message, args.log_file, args.quiet)
step_list.append('download_prot_accession2taxid_file')
message = 'File fastaid2LCAtaxid will be created.'
shared.give_user_feedback(message, args.log_file, args.quiet)
step_list.append('make_fastaid2LCAtaxid_file')
else:
message = ('Fastaid2LCAtaxid found: {0}.'.format(
args.fastaid2LCAtaxid_file))
shared.give_user_feedback(message, args.log_file, args.quiet)
if not args.prot_accession2taxid_file:
message = 'Prot.accession2taxid file will not be needed.'
shared.give_user_feedback(message, args.log_file, args.quiet)
if not args.taxids_with_multiple_offspring_file:
message = 'File taxids_with_multiple_offspring will be created.'
shared.give_user_feedback(message, args.log_file, args.quiet)
step_list.append('make_taxids_with_multiple_offspring_file')
else:
message = 'Taxids_with_multiple_offspring found: {0}'.format(
args.taxids_with_multiple_offspring_file)
shared.give_user_feedback(message, args.log_file, args.quiet)
if not args.nr_file and whether_to_download_nr is False:
# This is pushed here just for the logic of the user.
message = ('NOTE: Database folder contains all the necessary files '
'except for nr.gz. Since nr.gz is not used by CAT or BAT, '
'this is fine.')
shared.give_user_feedback(message, args.log_file, args.quiet)
if (not os.path.isdir(args.taxonomy_folder)
and not os.path.isdir(args.database_folder)):
message = (
'\n-----------------\n\n'
'WARNING: no taxonomy or database folder was found. CAT '
'prepare will create them fresh. Are you sure you are linking '
'to existing folders?')
shared.give_user_feedback(message,
args.log_file,
args.quiet,
show_time=False)
if 'make_fastaid2LCAtaxid_file' in step_list:
# Check memory.
memory_bottleneck(args)
if len(step_list) == 0:
message = ('All necessary files are found. Existing database does not '
'need any more work...')
shared.give_user_feedback(message,
args.log_file,
args.quiet,
show_time=False)
sys.exit(0)
else:
message = 'Ready to fly!\n\n-----------------\n'
shared.give_user_feedback(message,
args.log_file,
args.quiet,
show_time=False)
prepare(step_list, args)
return
def run_fresh(args):
message = '# CAT v{0}.'.format(about.__version__)
shared.give_user_feedback(message,
args.log_file,
args.quiet,
show_time=False)
message = (
'\n'
'CAT prepare is running, constructing a fresh database.\n'
'Rawr!\n\n'
'WARNING: preparing the database files may take a couple of hours.'
'\n\n'
'Supplied command: {0}\n\n'
'Taxonomy folder: {1}\n'
'Database folder: {2}\n'
'Log file: {3}\n\n'
'-----------------\n'.format(' '.join(sys.argv), args.taxonomy_folder,
args.database_folder, args.log_file))
shared.give_user_feedback(message,
args.log_file,
args.quiet,
show_time=False)
# Check diamond path.
error = check.check_diamond_binaries(args.path_to_diamond, args.log_file,
args.quiet)
if error:
sys.exit(1)
if os.path.isdir(args.taxonomy_folder):
if args.nodes_dmp or args.names_dmp or args.prot_accession2taxid_file:
message = (
'taxonomy folder {0} exists already and contains taxonomy '
'files. Supply a novel or empty folder if you want '
'to start fresh, or run CAT prepare --existing.'.format(
args.taxonomy_folder))
shared.give_user_feedback(message,
args.log_file,
args.quiet,
error=True)
sys.exit(1)
message = ('Taxonomy folder exists already. Taxonomy files will be '
'downloaded to it.')
shared.give_user_feedback(message, args.log_file, args.quiet)
if os.path.isdir(args.database_folder):
if (args.nr_file or args.diamond_database or args.fastaid2LCAtaxid_file
or args.taxids_with_multiple_offspring_file):
message = (
'database folder {0} exists already and contains database '
'files. Supply a novel or empty folder if you want to '
'start fresh.'.format(args.database_folder))
shared.give_user_feedback(message,
args.log_file,
args.quiet,
error=True)
sys.exit(1)
message = ('Database folder exists already. Database file will be '
'downloaded to it / constructed in it.')
shared.give_user_feedback(message, args.log_file, args.quiet)
# Check memory.
memory_bottleneck(args)
step_list = [
'download_taxonomy_files', 'download_prot_accession2taxid_file',
'download_nr', 'make_diamond_database', 'make_fastaid2LCAtaxid_file',
'make_taxids_with_multiple_offspring_file'
]
prepare(step_list, args)
return
