Source code for cnvlib.core

"""CNV utilities."""
from __future__ import absolute_import, division, print_function
from builtins import map
from past.builtins import basestring

import contextlib
import logging
import os
import subprocess
import tempfile

# __________________________________________________________________________
# I/O helpers

[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: %s" % 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)"Moved existing file %s -> %s", fname, bak_fname) return True
[docs]@contextlib.contextmanager def temp_write_text(text, mode="w+b"): """Save text to a temporary file. NB: This won't work on Windows b/c the file stays open. """ with tempfile.NamedTemporaryFile(mode=mode) as tmp: tmp.write(text) tmp.flush() yield
# __________________________________________________________________________ # More helpers
[docs]def assert_equal(msg, **values): """Evaluate and compare two or more values for equality. Sugar for a common assertion pattern. Saves re-evaluating (and retyping) the same values for comparison and error reporting. Example: >>> assert_equal("Mismatch", expected=1, saw=len(['xx', 'yy'])) ... ValueError: Mismatch: expected = 1, saw = 2 """ ok = True key1, val1 = values.popitem() msg += ": %s = %r" % (key1, val1) for okey, oval in values.items(): msg += ", %s = %r" % (okey, oval) if oval != val1: ok = False if not ok: raise ValueError(msg)
[docs]def check_unique(items, title): """Ensure all items in an iterable are identical; return that one item.""" its = set(items) assert len(its) == 1, ("Inconsistent %s keys: %s" % (title, ' '.join(map(str, sorted(its))))) return its.pop()
[docs]def fbase(fname): """Strip directory and all extensions from a filename.""" base = os.path.basename(fname) # Gzip extension usually follows another extension if base.endswith('.gz'): base = base[:-3] # Cases to drop more than just the last dot known_multipart_exts = ( '.antitargetcoverage.cnn', '.targetcoverage.cnn', '.antitargetcoverage.csv', '.targetcoverage.csv', # Pipeline suffixes '.recal.bam', '.deduplicated.realign.bam', ) for ext in known_multipart_exts: if base.endswith(ext): base = base[:-len(ext)] break else: base = base.rsplit('.', 1)[0] return base