autometa-coverage doesn't accept gzipped input

[jason-c-kwan]

Current Behavior

When giving autometa-coverage a gzipped input fasta, we get an error. Users might do this if they are trying to work on the example datasets and they feel like skipping the length-filtering step or just want to use the filtered fasta we provide.

Steps to Reproduce

autometa-coverage --from-spades --assembly metagenome.filtered.fna.gz --out coverage_table.tsv

Traceback (most recent call last):
  File "/opt/conda/bin/autometa-coverage", line 33, in <module>
    sys.exit(load_entry_point('Autometa==2.0a0', 'console_scripts', 'autometa-coverage')())
  File "/opt/conda/lib/python3.8/site-packages/Autometa-2.0a0-py3.8.egg/autometa/common/coverage.py", line 296, in main
    records = [rec for rec in SeqIO.parse(args.assembly, "fasta")]
  File "/opt/conda/lib/python3.8/site-packages/Autometa-2.0a0-py3.8.egg/autometa/common/coverage.py", line 296, in <listcomp>
    records = [rec for rec in SeqIO.parse(args.assembly, "fasta")]
  File "/opt/conda/lib/python3.8/site-packages/Bio/SeqIO/Interfaces.py", line 73, in __next__
    return next(self.records)
  File "/opt/conda/lib/python3.8/site-packages/Bio/SeqIO/FastaIO.py", line 198, in iterate
    for title, sequence in SimpleFastaParser(handle):
  File "/opt/conda/lib/python3.8/site-packages/Bio/SeqIO/FastaIO.py", line 47, in SimpleFastaParser
    for line in handle:
  File "/opt/conda/lib/python3.8/codecs.py", line 322, in decode
    (result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte

Expected Behavior

We should get no errors, and the file should be read zipped.

Environment Information

autometa --check-dependencies --debug

Run Information

cat path/to/your/input/metagenome.config

cat path/to/your/outdir/metagenome.config

Log information generated by autometa. If you have run autometa with the --log flag, e.g. autometa --log then use the contents of the logfile.