mrmatrix more flexible

[mccalluc]

Fix #63, Fix #64

Description

What was changed in this pull request?

• Removed the option to take TSV from STDIN: This is difficult, because we need to know the the full size before we start reading out the data: If only the width matters, no problem, but if it could be taller than it is wide, then two passes really are necessary, and I'm not sure how this would be done memory efficiently if we only have STDIN.
• Use built-in tsv parsing.
• Add new command-line arguments.
• Fix all linting problems in these two files, and enforce it in travis

$ python ./scripts/tsv_to_mrmatrix.py --help
usage: tsv_to_mrmatrix.py [-h] [-d D] [-n N] [-s] [-l] input_file output_file

Given a tab-delimited file, produces an HDF5 file with mrmatrix ("multi-
resolution matrix") structure: Under the "resolutions" group are datasets,
named with successive powers of 2, which represent successively higher
aggregations of the input.

positional arguments:
  input_file           TSV file path
  output_file          HDF5 file

optional arguments:
  -h, --help           show this help message and exit
  -d D, --delimiter D  Delimiter; defaults to tab
  -n N, --first-n N    Only read first N columns from first N rows
  -s, --square         Row labels are assumed to match column labels
  -l, --labelled       TSV Matrix has column and row labels

Tests I wrote earlier still pass, but I need to add tests of newer functionality.

Why is it necessary?

The data I'll want to load is taller than it is wide, and has no row or column labels. This tests that case.

Checklist

• Unit tests added or updated
• Updated CHANGELOG.md

[mccalluc]

@pkerpedjiev : Let me resolve the conflicts and get back to you about the other questions...

[mccalluc]

The 3d1aca9 pr build failed because it couldn't download... Hopefully just a transient network issue on Travis.