Correct bed sort, moved stuff to libs and wrappers

install.sh

+#!/bin/sh
+python3.6 setup.py build_ext
+pip3.6 install -e .

libhts/__init__.py

+from .libhts import do_deseq2

libhts/libhts.py

+import pandas as pd
+from rpy2.robjects import r, pandas2ri, Formula, StrVector
+as_df = r("as.data.frame")
+from rpy2.robjects.packages import importr
+deseq2 = importr("DESeq2")
+
+def do_deseq2(cond_names, conditions, counts_data,
+              formula=None, contrast=None, deseq2_args=None):
+    """Runs a DESeq2 differential expression analysis."""
+    if formula is None:
+        formula = Formula("~ lib")
+    if contrast is None:
+        contrast = StrVector(["lib", MUT, REF])
+    if deseq2_args is None:
+        deseq2_args = {"betaPrior" : True, "addMLE" : True, "independentFiltering" : True}
+    col_data = pd.DataFrame(conditions).assign(cond_name=pd.Series(cond_names).values)
+    col_data.set_index("cond_name", inplace=True)
+    # In case we want contrasts between factor combinations
+    if ("lib" in col_data.columns) and ("treat" in col_data.columns):
+        col_data = col_data.assign(
+            lib_treat = ["%s_%s" % (lib, treat) for (lib, treat) in zip(
+                col_data["lib"], col_data["treat"])])
+    # http://stackoverflow.com/a/31206596/1878788
+    pandas2ri.activate()  # makes some conversions automatic
+    # r_counts_data = pandas2ri.py2ri(counts_data)
+    # r_col_data = pandas2ri.py2ri(col_data)
+    # r.DESeqDataSetFromMatrix(countData=r_counts_data, colData=r_col_data, design=Formula("~lib"))
+    dds = deseq2.DESeqDataSetFromMatrix(
+        countData=counts_data,
+        colData=col_data,
+        design=formula)
+    dds = deseq2.DESeq(dds, betaPrior=deseq2_args["betaPrior"])
+    res = pandas2ri.ri2py(as_df(deseq2.results(
+        dds,
+        contrast=contrast,
+        addMLE=deseq2_args["addMLE"],
+        independentFiltering=deseq2_args["independentFiltering"])))
+    res.index = counts_data.index
+    return res
+

setup.py

+from setuptools import setup, find_packages
+#from Cython.Build import cythonize
+
+name = "libhts"
+
+# Adapted from Biopython
+__version__ = "Undefined"
+for line in open("%s/__init__.py" % name):
+    if (line.startswith('__version__')):
+        exec(line.strip())
+
+
+setup(
+    name=name,
+    version=__version__,
+    description="Miscellaneous things to process high throughput sequencing data.",
+    author="Blaise Li",
+    author_email="blaise.li@normalesup.org",
+    license="MIT",
+    packages=find_packages())
+    #ext_modules = cythonize("libsmallrna/libsmallrna.pyx"),
+    #install_requires=["cytoolz"],
+    #zip_safe=False