def glimmerHMM(tool_dir, fasta_fpath, out_fpath, gene_lengths, err_path, tmp_dir, index):
def run(contig_path, tmp_path):
with open(err_path, 'a') as err_file:
return_code = qutils.call_subprocess(
[tool_exec, contig_path, '-d', trained_dir, '-g', '-o', tmp_path],
stdout=err_file,
stderr=err_file,
indent=' ' + qutils.index_to_str(index) + ' ')
return return_code
tool_exec = os.path.join(tool_dir, 'glimmerhmm')
# Note: why arabidopsis? for no particular reason, really.
trained_dir = os.path.join(tool_dir, 'trained', 'arabidopsis')
contigs = {}
gffs = []
base_dir = tempfile.mkdtemp(dir=tmp_dir)
for seq_num, (ind, seq) in enumerate(read_fasta(fasta_fpath)):
seq_num = str(seq_num)
ind = ind[:qutils.MAX_CONTIG_NAME_GLIMMER]
contig_path = os.path.join(base_dir, seq_num + '.fasta')
gff_path = os.path.join(base_dir, seq_num + '.gff')
write_fasta(contig_path, [(ind, seq)])
if run(contig_path, gff_path) == 0:
gffs.append(gff_path)
contigs[ind] = seq
if not gffs:
return None, None, None, None
out_gff_fpath = out_fpath + '_genes.gff' + ('.gz' if not qconfig.no_gzip else '')
out_gff_path = merge_gffs(gffs, out_gff_fpath)
unique, total = set(), 0
genes = []
for contig, gene_id, start, end, strand in parse_gff(out_gff_path):
total += 1
if strand == '+':
gene_seq = contigs[contig][start - 1:end]
else:
gene_seq = rev_comp(contigs[contig][start - 1:end])
if gene_seq not in unique:
unique.add(gene_seq)
gene = Gene(contig=contig, start=start, end=end, strand=strand, seq=gene_seq)
gene.is_full = gene.start > 1 and gene.end < len(contigs[contig])
genes.append(gene)
full_cnt = [sum([gene.end - gene.start >= threshold for gene in genes if gene.is_full]) for threshold in gene_lengths]
partial_cnt = [sum([gene.end - gene.start >= threshold for gene in genes if not gene.is_full]) for threshold in gene_lengths]
if OUTPUT_FASTA:
out_fasta_fpath = out_fpath + '_genes.fasta'
add_genes_to_fasta(genes, out_fasta_fpath)
if not qconfig.debug:
shutil.rmtree(base_dir)
#return out_gff_path, out_fasta_path, len(unique), total, cnt
return out_gff_path, genes, len(unique), total, full_cnt, partial_cnt
def glimmerHMM(tool_dir, fasta_fpath, out_fpath, gene_lengths, err_path, tmp_dir, index):
def run(contig_path, tmp_path):
with open(err_path, 'a') as err_file:
return_code = qutils.call_subprocess(
[tool_exec, contig_path, '-d', trained_dir, '-g', '-o', tmp_path],
stdout=err_file,
stderr=err_file,
indent=' ' + qutils.index_to_str(index) + ' ')
return return_code
tool_exec = os.path.join(tool_dir, 'glimmerhmm')
# Note: why arabidopsis? for no particular reason, really.
trained_dir = os.path.join(tool_dir, 'trained', 'arabidopsis')
contigs = {}
gffs = []
base_dir = tempfile.mkdtemp(dir=tmp_dir)
for seq_num, (ind, seq) in enumerate(read_fasta(fasta_fpath)):
seq_num = str(seq_num)
ind = ind[:qutils.MAX_CONTIG_NAME_GLIMMER]
contig_path = os.path.join(base_dir, seq_num + '.fasta')
gff_path = os.path.join(base_dir, seq_num + '.gff')
write_fasta(contig_path, [(ind, seq)])
if run(contig_path, gff_path) == 0:
gffs.append(gff_path)
contigs[ind] = seq
if not gffs:
return None, None, None, None
out_gff_fpath = out_fpath + '_genes.gff' + ('.gz' if not qconfig.no_gzip else '')
out_gff_path = merge_gffs(gffs, out_gff_fpath)
unique, total = set(), 0
genes = []
for contig, gene_id, start, end, strand in parse_gff(out_gff_path):
total += 1
if strand == '+':
gene_seq = contigs[contig][start - 1:end]
else:
gene_seq = rev_comp(contigs[contig][start - 1:end])
if gene_seq not in unique:
unique.add(gene_seq)
gene = Gene(contig=contig, start=start, end=end, strand=strand, seq=gene_seq)
gene.is_full = gene.start > 1 and gene.end < len(contigs[contig])
genes.append(gene)
full_cnt = [sum([gene.end - gene.start >= threshold for gene in genes if gene.is_full]) for threshold in gene_lengths]
partial_cnt = [sum([gene.end - gene.start >= threshold for gene in genes if not gene.is_full]) for threshold in gene_lengths]
if OUTPUT_FASTA:
out_fasta_fpath = out_fpath + '_genes.fasta'
add_genes_to_fasta(genes, out_fasta_fpath)
if not qconfig.debug:
shutil.rmtree(base_dir)
#return out_gff_path, out_fasta_path, len(unique), total, cnt
return out_gff_path, genes, len(unique), total, full_cnt, partial_cnt