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
import sys
import os
sys.path.append(os.path.join(os.path.abspath(sys.path[0]), '../'))
import quast_libs
from quast_libs import fastaparser
if len(sys.argv) <= 3 or len(sys.argv) >= 6:
print("Returns [reverse-complement] sequence from START to END position from each entry of input fasta")
print("Usage: " + sys.argv[0] + " <input fasta> <START> <END, -1 for the end> [any string -- optional parameter for reverse-complement]")
sys.exit()
inp=sys.argv[1]
start=int(sys.argv[2])
end=int(sys.argv[3])
reverse = False
if len(sys.argv) == 5:
reverse = True
for tup in fastaparser.read_fasta(inp):
cur_start = min(start, len(tup[1]))
if end == -1:
cur_end = len(tup[1])
else:
cur_end = min(end, len(tup[1]))
print (">" + tup[0] + "_cropped_" + str(cur_start) + "_" + str(cur_end))
if reverse:
print (fastaparser.rev_comp(tup[1][cur_start - 1 : cur_end]))
else:
print (tup[1][cur_start - 1 : cur_end])
