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 ind, seq in read_fasta(fasta_fpath):
ind = re.sub('[/. ]', '_', ind)
contig_path = os.path.join(base_dir, ind + '.fasta')
gff_path = os.path.join(base_dir, ind + '.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_path = merge_gffs(gffs, out_fpath + '_genes.gff')
unique, total = set(), 0
genes = []
cnt = [0] * len(gene_lengths)
for contig, gene_id, start, end, strand in parse_gff(out_gff_path):
total += 1
if strand == '+':
gene_seq = contigs[contig][start:end + 1]
else:
gene_seq = rev_comp(contigs[contig][start:end + 1])
if gene_seq not in unique:
unique.add(gene_seq)
genes.append((gene_id, gene_seq))
for idx, gene_length in enumerate(gene_lengths):
cnt[idx] += end - start > gene_length
if OUTPUT_FASTA:
out_fasta_path = out_fpath + '_genes.fasta'
write_fasta(out_fasta_path, genes)
if not qconfig.debug:
shutil.rmtree(base_dir)
#return out_gff_path, out_fasta_path, len(unique), total, cnt
return out_gff_path, len(unique), total, 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 ind, seq in read_fasta(fasta_fpath):
contig_path = os.path.join(base_dir, ind + '.fasta')
gff_path = os.path.join(base_dir, ind + '.gff')
write_fasta(contig_path, [(ind, seq)])
if run(contig_path, gff_path) == 0:
gffs.append(gff_path)
contigs[ind] = seq
if not gffs:
logger.error(
'Glimmer failed running Glimmer for %s. ' + ('Run with the --debug option'
' to see the command line.' if not qconfig.debug else '') % qutils.label_from_fpath(fasta_fpath))
return None, None, None, None
out_gff_path = merge_gffs(gffs, out_fpath + '_genes.gff')
unique, total = set(), 0
genes = []
cnt = [0] * len(gene_lengths)
for contig, gene_id, start, end, strand in parse_gff(out_gff_path):
total += 1
if strand == '+':
gene_seq = contigs[contig][start:end + 1]
else:
gene_seq = rev_comp(contigs[contig][start:end + 1])
if gene_seq not in unique:
unique.add(gene_seq)
genes.append((gene_id, gene_seq))
for idx, gene_length in enumerate(gene_lengths):
cnt[idx] += end - start > gene_length
if OUTPUT_FASTA:
out_fasta_path = out_fpath + '_genes.fasta'
write_fasta(out_fasta_path, genes)
if not qconfig.debug:
shutil.rmtree(base_dir)
#return out_gff_path, out_fasta_path, len(unique), total, cnt
return out_gff_path, len(unique), total, cnt
import sys
import os
sys.path.append(os.path.join(os.path.abspath(sys.path[0]), '../'))
import libs
from 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])