def summarise(args):
(input_file, output_file, contigs_fasta, force,
quiet) = check.convert_arguments(args)
if contigs_fasta == None:
summarise_bins(input_file, output_file, force, quiet)
else:
summarise_contigs(input_file, output_file, contigs_fasta, force, quiet)
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 add_names(args):
(input_file,
output_file,
taxonomy_folder,
only_official,
force,
quiet) = check.convert_arguments(args)
# Currently add_names does not allow for a log file.
log_file = None
message = '# CAT v{0}.'.format(about.__version__)
shared.give_user_feedback(message, log_file, quiet, show_time=False)
errors = []
errors.append(check.check_input_file(input_file, log_file, quiet))
if not force:
errors.append(check.check_output_file(output_file, log_file, quiet))
if True in errors:
sys.exit(1)
(nodes_dmp,
names_dmp,
prot_accession2taxid_file) = check.inspect_taxonomy_folder(taxonomy_folder)
(taxid2parent, taxid2rank) = tax.import_nodes(nodes_dmp, log_file, quiet)
taxid2name = tax.import_names(names_dmp, log_file, quiet)
message = 'Appending names...'
shared.give_user_feedback(message, log_file, quiet)
with open(input_file, 'r') as f1:
for line in f1:
if line.startswith('#'):
line = line.rstrip().split('\t')
try:
lineage_index = line.index('lineage')
except:
message = ('ERROR: {0} is not a supported classification '
'file.'.format(input_file))
shared.give_user_feedback(message,
log_file,
quiet,
error=True)
sys.exit(1)
try:
scores_index = line.index('lineage scores')
except:
scores_index = None
full_length = len(line)
break
else:
message = ('ERROR: {0} is not a supported classification file.'
''.format(input_file))
shared.give_user_feedback(message, log_file, quiet, error=True)
sys.exit(1)
with open(input_file, 'r') as f1, open(output_file, 'w') as outf1:
for line in f1:
line = line.rstrip()
if line.startswith('#'):
if only_official:
outf1.write('{0}\tsuperkingdom\tphylum\tclass\torder\t'
'family\tgenus\tspecies\n'.format(line))
else:
outf1.write('{0}\tfull lineage names\n'.format(line))
continue
line = line.split('\t')
if len(line) != full_length:
# Entry does not have a full annotation.
outf1.write('{0}\n'.format('\t'.join(line)))
continue
if (line[1].startswith('no taxid found') or
line[2].startswith('no taxid found')):
# ORF has database hits but the accession number is not found
# in the taxonomy files.
outf1.write('{0}\n'.format('\t'.join(line)))
continue
lineage = line[lineage_index].split(';')
if scores_index:
scores = line[scores_index].split(';')
else:
scores = None
if only_official:
names = tax.convert_to_official_names(lineage,
taxid2rank,
taxid2name,
scores)
else:
names = tax.convert_to_names(lineage,
taxid2rank,
taxid2name,
scores)
outf1.write('{0}\t{1}\n'.format('\t'.join(line), '\t'.join(names)))
message = 'Names written to {0}!'.format(output_file)
shared.give_user_feedback(message, log_file, quiet)
