def install_srna(species, gtf):
out_file = os.path.join(SRNASEQ_DIR, "srna-transcripts.gtf")
safe_makedir(SRNASEQ_DIR)
if not os.path.exists(out_file):
shutil.copyfile(gtf, out_file)
try:
from seqcluster import install
except ImportError:
raise ImportError("install seqcluster first, please.")
with chdir(SRNASEQ_DIR):
hairpin, miRNA = install._install_mirbase()
cmd = ("grep -A 2 {species} {hairpin} | grep -v '\-\-$' | tr U T > hairpin.fa")
do.run(cmd.format(**locals()), "set precursor.")
cmd = ("grep -A 1 {species} {miRNA} > miRNA.str")
do.run(cmd.format(**locals()), "set miRNA.")
shutil.rmtree("mirbase")
return out_file
def install_srna(species, gtf):
out_file = os.path.join(SRNASEQ_DIR, "srna-transcripts.gtf")
safe_makedir(SRNASEQ_DIR)
if not os.path.exists(out_file):
shutil.copyfile(gtf, out_file)
try:
from seqcluster import install
except ImportError:
raise ImportError("install seqcluster first, please.")
with chdir(SRNASEQ_DIR):
hairpin, miRNA = install._install_mirbase()
cmd = ("grep -A 2 {species} {hairpin} | grep -v '\-\-$' | tr U T > hairpin.fa")
do.run(cmd.format(**locals()), "set precursor.")
cmd = ("grep -A 1 {species} {miRNA} > miRNA.str")
do.run(cmd.format(**locals()), "set miRNA.")
shutil.rmtree("mirbase")
return out_file
def install_srna(species, gtf):
out_file = os.path.join(SRNASEQ_DIR, "srna-transcripts.gtf")
safe_makedir(SRNASEQ_DIR)
if gtf:
if not file_exists(out_file):
shutil.copyfile(gtf, out_file)
try:
from seqcluster import install
except ImportError:
raise ImportError("install seqcluster first, please.")
with chdir(SRNASEQ_DIR):
hairpin, miRNA = install._install_mirbase()
cmd = ("cat %s | awk '{if ($0~/>%s/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > hairpin.fa")
do.run(cmd % (hairpin, species), "set precursor.")
cmd = ("grep -A 1 {species} {miRNA} > miRNA.str")
do.run(cmd.format(**locals()), "set miRNA.")
shutil.rmtree("mirbase")
return out_file
def install_srna(species, gtf):
out_file = os.path.join(SRNASEQ_DIR, "srna-transcripts.gtf")
safe_makedir(SRNASEQ_DIR)
if gtf:
if not file_exists(out_file):
shutil.copyfile(gtf, out_file)
try:
from seqcluster import install
except ImportError:
raise ImportError("install seqcluster first, please.")
with chdir(SRNASEQ_DIR):
hairpin, miRNA = install._install_mirbase()
cmd = ("cat %s | awk '{if ($0~/>%s/){name=$0; print name} else if ($0~/^>/){name=0};if (name!=0 && $0!~/^>/){print $0;}}' | sed 's/U/T/g' > hairpin.fa")
do.run(cmd % (hairpin, species), "set precursor.")
cmd = ("grep -A 1 {species} {miRNA} > miRNA.str")
do.run(cmd.format(**locals()), "set miRNA.")
shutil.rmtree("mirbase")
return out_file
