This is to limit clutter from old analyses.

This is used to circumvent the change in behaviour in snakemake.
https://bitbucket.org/snakemake/snakemake/issues/956/placeholders-not-properly-matched-with

This is now used for degradation efficiency too.
The general concept is to compute a fold of TPM bewteen library types.
TE is for Ribo / RNA, DE is for Degradome / RNA.

Snakemake 5.2.2 now checks that log file names have enough wildcards.

The notebook contains code simulating pairs of read sets of known
distances and tests the script computing the distances.

Plotting 5UTR, CDS and 3UTR on the same graph can help discover
interesting behaviours.

Also helped overcome recursion limit issue with clustermap.

This should be easier to maintain than a manually-written list.

This also seems to make it faster.

The filtering may be very slow if there are many genes, because it is
based on as many calls to AlignmentFile.fetch. Maybe it could be faster
to use BedTool.intersect, depending on the number of intervals.

It needs a list of identifiers and an annotation file, and generates a
pybedtools.BedTool.

Also added tests.

The script currently takes two bam files and gives the distribution of
distances between reads in one "degradome" file and their antisense
neighbours in a "small RNA" file.

This is meant to be used to compute distances between mapping positions,
for instance that of degradome reads and small RNAs.

The pipeline only maps and counts aligned reads in biotypes.

Added function to compute seed disposition from bowtie2 settings.

From the results, it seems that these settings are OK for the smallest
size range, but not for longer reads.

The ValueError was:
`Invalid file path or buffer object type: <class 'snakemake.io.Namedlist'>`

This was due to an extra comma at the end of the return of `source_norm_file`.

Some wildcard did not get properly substituted.

When low quality zones are kept for deduplication, they later need to be
trimmed.