def make_phylip_seq_dist_mat(inseqs, alphabet, tmp_path = None):
commands = "2\ny\n"
with tmp_directory(dir=tmp_path, rm_dir=False) as r_path:
with push_dir(r_path):
with open('cmd_file', 'w') as cmd_handle:
cmd_handle.write(commands)
cmd_handle = open('cmd_file')
with open('infile', 'w') as handle:
trans_names = write_phylip_seqs(inseqs, handle, alphabet = alphabet)
if alphabet == generic_protein:
cmd = 'phylip protdist'
elif alphabet == generic_dna:
cmd = 'phylip dnadist'
else:
raise KeyError, 'Unknown alphabet.'
cmd = shlex.split(cmd)
try:
check_call(cmd, stdin = cmd_handle)
except:
print r_path
raise KeyError
with open('outfile') as handle:
dist_data = handle.read()
return trans_names, dist_data
def make_phylip_tree(dist_data, tmp_path = None):
commands = "2\n3\ny\n"
with tmp_directory(dir=tmp_path, rm_dir=True) as r_path:
with push_dir(r_path):
with open('cmd_file', 'w') as cmd_handle:
cmd_handle.write(commands)
cmd_handle = open('cmd_file')
with open('infile', 'w') as handle:
handle.write(dist_data)
cmd = shlex.split('phylip neighbor')
check_call(cmd, stdin = cmd_handle)
with open('outtree') as handle:
tree = dendropy.Tree.get_from_stream(handle, schema='newick')
return tree
def make_pdf(input_notebook_path, output_pdf):
"""Converts a ipyp notebook to a pdf"""
notebook_fname = input_notebook_path.rsplit(os.sep, 1)[-1]
notebook_base = notebook_fname.rsplit('.', 1)[0]
with tmp_directory() as tmp_path:
with tmp_changedir(tmp_path):
new_notebook_path = os.path.join(tmp_path, notebook_fname)
new_tex_path = os.path.join(tmp_path, notebook_base+'.tex')
new_pdf_path = os.path.join(tmp_path, notebook_base+'.pdf')
shutil.copy(input_notebook_path, new_notebook_path)
run_nbconvert(new_notebook_path)
run_latex(new_tex_path)
shutil.move(new_pdf_path, output_pdf)
def align_with_lastz(input_seqs, ref_seqs):
"""Aligns set of query sequences with a reference."""
with tmp_directory() as tmp_dir:
seq_file = os.path.join(tmp_dir, "query.fasta")
ref_file = os.path.join(tmp_dir, "ref.fasta")
out_file = os.path.join(tmp_dir, "res.fasta")
with open(seq_file, "w") as handle:
fasta_writer(handle, input_seqs)
with open(ref_file, "w") as handle:
fasta_writer(handle, ref_seqs)
call_lastz(seq_file, ref_file, out_file)
with open(out_file) as handle:
return list(SAMreader(handle))