def _msa_filter_by_taxa(self, concatenated_file, gtdb_taxonomy, taxa_filter, outgroup_taxon):
"""Filter GTDB MSA filtered to specified taxa."""
msa = read_fasta(concatenated_file)
self.logger.info(
'Read concatenated alignment for %d GTDB genomes.' % len(msa))
if taxa_filter is not None:
taxa_to_keep = set(taxa_filter.split(','))
if outgroup_taxon not in taxa_to_keep and outgroup_taxon is not None:
taxa_to_keep.add(outgroup_taxon)
filtered_genomes = 0
for genome_id, taxa in gtdb_taxonomy.iteritems():
common_taxa = taxa_to_keep.intersection(taxa)
if len(common_taxa) == 0:
if genome_id in msa:
del msa[genome_id]
filtered_genomes += 1
self.logger.info(
'Filtered %d taxa based on assigned taxonomy.' % filtered_genomes)
return msa
def trim_msa(self, untrimmed_msa, mask_type, maskid, output_file):
if maskid == 'bac' and mask_type == 'reference':
mask = os.path.join(Config.MASK_DIR, Config.MASK_BAC120)
elif maskid == 'arc' and mask_type == 'reference':
mask = os.path.join(Config.MASK_DIR, Config.MASK_AR122)
elif mask_type == 'file':
mask = maskid
with open(mask, 'r') as f:
maskstr = f.readline()
outfwriter = open(output_file, 'w')
dict_genomes = read_fasta(untrimmed_msa, False)
for k, v in dict_genomes.iteritems():
aligned_seq = ''.join([v[i] for i in xrange(
0, len(maskstr)) if maskstr[i] == '1'])
fasta_outstr = ">%s\n%s\n" % (k, aligned_seq)
outfwriter.write(fasta_outstr)
outfwriter.close()
return True
def run(self, msa_file, marker_list):
"""Randomly select a subset of columns from the MSA of each marker."""
# read multiple sequence alignment
self.logger.info('Reading multiple sequence alignment.')
msa = read_fasta(msa_file, False)
self.logger.info('Read MSA for %d genomes.' % len(msa))
filtered_seqs, pruned_seqs = self.trim(msa, marker_list)
self.logger.info(
'Removed %d taxa have amino acids in <%.1f%% of columns in filtered MSA.'
% (len(pruned_seqs), self.min_perc_aa))
# write out trimmed sequences
filter_file = open(os.path.join(self.output_dir, "filtered_msa.faa"),
'w')
for gid, seq in filtered_seqs.items():
fasta_outstr = ">%s\n%s\n" % (gid, seq)
filter_file.write(fasta_outstr)
filter_file.close()
self.logger.info('Done.')
def _report_identified_marker_genes(self, gene_dict, outdir, marker_gene_dir, prefix):
"""Report statistics for identified marker genes."""
translation_table_file = open(os.path.join(outdir, PATH_TLN_TABLE_SUMMARY.format(prefix=prefix)), "w")
bac_outfile = open(os.path.join(outdir, PATH_BAC120_MARKER_SUMMARY.format(prefix=prefix)), "w")
arc_outfile = open(os.path.join(outdir, PATH_AR122_MARKER_SUMMARY.format(prefix=prefix)), "w")
header = "Name\tnumber_unique_genes\tnumber_multiple_genes\tnumber_missing_genes\tlist_unique_genes\tlist_multiple_genes\tlist_missing_genes\n"
bac_outfile.write(header)
arc_outfile.write(header)
# gather information for all marker genes
marker_dbs = {"PFAM": PFAM_TOP_HIT_SUFFIX, "TIGR": TIGRFAM_TOP_HIT_SUFFIX}
marker_bac_list_original = []
for db_marker in Config.BAC120_MARKERS.keys():
marker_bac_list_original.extend([marker.replace(".HMM", "").replace(".hmm", "")
for marker in Config.BAC120_MARKERS[db_marker]])
marker_arc_list_original = []
for db_marker in Config.AR122_MARKERS.keys():
marker_arc_list_original.extend([marker.replace(".HMM", "").replace(".hmm", "")
for marker in Config.AR122_MARKERS[db_marker]])
for db_genome_id, info in gene_dict.items():
unique_genes_bac, multi_hits_bac, missing_genes_bac = [], [], []
unique_genes_arc, multi_hits_arc, missing_genes_arc = [], [], []
gene_bac_dict, gene_arc_dict = {}, {}
path = info.get("aa_gene_path")
for _marker_db, marker_suffix in marker_dbs.iteritems():
# get all gene sequences
protein_file = str(path)
tophit_path = protein_file.replace(PROTEIN_FILE_SUFFIX, marker_suffix)
# we load the list of all the genes detected in the genome
all_genes_dict = read_fasta(protein_file, False)
# Prodigal adds an asterisks at the end of each called genes.
# These asterisks sometimes appear in the MSA, which can be
# an issue for some downstream software
for seq_id, seq in all_genes_dict.iteritems():
if seq[-1] == '*':
all_genes_dict[seq_id] = seq[:-1]
# we store the tophit file line by line and store the
# information in a dictionary
with open(tophit_path) as tp:
# first line is header line
tp.readline()
for line_tp in tp:
linelist = line_tp.split("\t")
genename = linelist[0]
sublist = linelist[1]
if ";" in sublist:
diff_markers = sublist.split(";")
else:
diff_markers = [sublist]
for each_mark in diff_markers:
sublist = each_mark.split(",")
markerid = sublist[0]
if (markerid not in marker_bac_list_original and
markerid not in marker_arc_list_original):
continue
if markerid in marker_bac_list_original:
if markerid in gene_bac_dict:
gene_bac_dict.get(markerid)[
"multihit"] = True
else:
gene_bac_dict[markerid] = {
"gene": genename,
"multihit": False}
if markerid in marker_arc_list_original:
if markerid in gene_arc_dict:
gene_arc_dict.get(markerid)[
"multihit"] = True
else:
gene_arc_dict[markerid] = {
"gene": genename,
"multihit": False}
for mid in marker_bac_list_original:
if mid not in gene_bac_dict:
missing_genes_bac.append(mid)
elif gene_bac_dict[mid]["multihit"]:
multi_hits_bac.append(mid)
else:
unique_genes_bac.append(mid)
for mid in marker_arc_list_original:
if mid not in gene_arc_dict:
missing_genes_arc.append(mid)
elif gene_arc_dict[mid]["multihit"]:
multi_hits_arc.append(mid)
else:
unique_genes_arc.append(mid)
bac_outfile.write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\n".format(db_genome_id,
len(unique_genes_bac),
len(multi_hits_bac),
len(missing_genes_bac),
','.join(
unique_genes_bac),
','.join(
multi_hits_bac),
','.join(missing_genes_bac)))
arc_outfile.write("{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\n".format(db_genome_id,
len(unique_genes_arc),
len(multi_hits_arc),
len(missing_genes_arc),
','.join(
unique_genes_arc),
','.join(
multi_hits_arc),
','.join(missing_genes_arc)))
translation_table_file.write('{}\t{}\n'.format(
db_genome_id, info.get("best_translation_table")))
bac_outfile.close()
arc_outfile.close()
translation_table_file.close()
# Create a symlink to store the summary files in the root.
os.symlink(PATH_BAC120_MARKER_SUMMARY.format(prefix=prefix),
os.path.join(outdir, os.path.basename(PATH_BAC120_MARKER_SUMMARY.format(prefix=prefix))))
os.symlink(PATH_AR122_MARKER_SUMMARY.format(prefix=prefix),
os.path.join(outdir, os.path.basename(PATH_AR122_MARKER_SUMMARY.format(prefix=prefix))))
os.symlink(PATH_TLN_TABLE_SUMMARY.format(prefix=prefix),
os.path.join(outdir, os.path.basename(PATH_TLN_TABLE_SUMMARY.format(prefix=prefix))))
