Parallel version using Pool.imap_unordered.

The small RNA reads are transmitted via a Queue in fastq format to a
function that writes them to a file.

To avoid wasting too much time in interprocess communication, the
annotation generator is buffered, and counting functions that work on
these buffers of annotation information are now used.

These functions have to be imported from libsmallrna in order to be
picklable (for multiprocessing) under cProfiling.

libsmallrna/__init__.py

+from .libsmallrna import has_pi_signature, has_endosi_signature, has_26G_signature, has_csr1_endosi_signature, count_annot, count_annots, count_pimi, count_pimis, count_si, count_sis, count_nucl, count_first_base, count_first_bases, add_compositions, add_results, Composition, get_read_info

setup.py

+from setuptools import setup
+from Cython.Build import cythonize
+
+setup(
+    name="libsmallrna",
+    version="0.1",
+    description="Miscellaneous things to deal with small RNA",
+    author="Blaise Li",
+    author_email="blaise.li@normalesup.org",
+    license="MIT",
+    # packages=["libsmallrna"],
+    ext_modules = cythonize("libsmallrna/libsmallrna.pyx"),
+    install_requires=["cytoolz"],
+    zip_safe=False)