Renamed fq_demux to qaf-demux, reorganizations.

fastq-demultiplexing/Python/fq_demux.py → fastq-demultiplexing/Python/bin/qaf-demux

@@ -3,13 +3,16 @@
 """This program demultiplexes fastq data based on a given list of
 barcodes and a barcode start position. It tries to assign each fastq
 record to the most likely barcode, taking into account the sequence
-qualities (interpreted as being sanger-encoded)."""
+qualities (interpreted as being sanger-encoded).
+
+Known similar approach: https://github.com/grenaud/deML
+"""
 
 import argparse
 import fileinput
 import os
 from itertools import islice
-
+# from qaf_demux.libqafdemux import parse_fastq
 
 OPD = os.path.dirname
 OPJ = os.path.join
@@ -85,13 +88,22 @@ def main():
         bpp = bc_prob_profile(seq, qual)
 
         def prob(barcode):
+            # TODO: handle N correctly
             bc_prob = 1
             nb_diff = 0
             for ((seq_letter, prob_err), bc_letter) in zip(bpp, barcode):
                 if seq_letter == bc_letter:
+                    # This position's contribution to the
+                    # probability for the barcode is the
+                    # probability that this letter is correct
                     bc_prob *= (1 - prob_err)
                 else:
                     nb_diff += 1
+                    # This position's contribution to the
+                    # probability for the barcode is the
+                    # probability that this letter is not correct
+                    # and that the real one is the one among the
+                    # three other that actually is bc_letter
                     bc_prob *= (prob_err / 3)
             return bc_prob, nb_diff
         return prob

fastq-demultiplexing/Python/install.sh

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

fastq-demultiplexing/Python/setup.py

+from setuptools import setup, find_packages
+#from Cython.Build import cythonize
+
+# Adapted from Biopython
+__version__ = "0.1"
+
+
+setup(
+    name="qaf_demux",
+    #version=libworkflows.__version__,
+    version=__version__,
+    description=".",
+    author="Blaise Li",
+    author_email="blaise.li__github@nsup.org",
+    license="MIT",
+    packages=find_packages(),
+    scripts=["bin/qaf-demux"])#,
+    #ext_modules = cythonize("qaf_demux/libqafdemux.pyx"),
+    #install_requires=["cytoolz"],
+    #zip_safe=False)