Source code for cnvlib.ngfrills

"""NGS utilities."""
from __future__ import absolute_import, division, print_function

import contextlib
import os
import subprocess
import sys
import tempfile

from Bio._py3k import basestring, map

from .faidx import *
from .regions import *
from .samutil import *
from .shared import *
from .vcf import *

# __________________________________________________________
# Shell

[docs]def call_quiet(*args): """Safely run a command and get stdout; print stderr if there's an error. Like subprocess.check_output, but silent in the normal case where the command logs unimportant stuff to stderr. If there is an error, then the full error message(s) is shown in the exception message. """ # args = map(str, args) if not len(args): raise ValueError("Must supply at least one argument (the command name)") try: proc = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE) except OSError as exc: raise RuntimeError("Could not find the executable %r" % args[0] + " -- is it installed correctly?" + "\n(Original error: %s)" % exc) out, err = proc.communicate() if proc.returncode != 0: raise RuntimeError("Subprocess command failed:\n$ %s\n\n%s" % (' '.join(args), err)) return out
[docs]def ensure_path(fname): """Create dirs and move an existing file to avoid overwriting, if necessary. If a file already exists at the given path, it is renamed with an integer suffix to clear the way. """ if '/' in os.path.normpath(fname): # Ensure the output directory exists dname = os.path.dirname(os.path.abspath(fname)) if dname and not os.path.isdir(dname): try: os.makedirs(dname) except OSError as exc: raise OSError("Output path " + fname + " contains a directory " + dname + " that cannot be created: " + str(exc)) if os.path.isfile(fname): # Add an integer suffix to the existing file name cnt = 1 bak_fname = "%s.%d" % (fname, cnt) while os.path.isfile(bak_fname): cnt += 1 bak_fname = "%s.%d" % (fname, cnt) os.rename(fname, bak_fname) echo("Moved existing file", fname, "->", bak_fname) return True
[docs]def safe_write(outfile, verbose=True): """Write to a filename or file-like object with error handling. If given a file name, open it. If the path includes directories that don't exist yet, create them. If given a file-like object, just pass it through. """ if isinstance(outfile, basestring): dirname = os.path.dirname(outfile) if dirname and not os.path.isdir(dirname): os.mkdir(dirname) echo("Created directory", dirname) with open(outfile, 'w') as handle: yield handle else: yield outfile # Log the output path, if possible if verbose: if isinstance(outfile, basestring): outfname = outfile elif hasattr(outfile, 'name') and outfile not in (sys.stdout, sys.stderr): outfname = else: # Probably stdout or stderr -- don't ruin the pipeline return echo("Wrote", outfname)
[docs]def temp_write_text(text): """Save text to a temporary file. NB: This won't work on Windows b/c the file stays open. """ with tempfile.NamedTemporaryFile() as tmp: tmp.write(text) tmp.flush() yield