Update filter to use new IO interface

augur/filter.py

@@ -14,6 +14,7 @@
 import treetime.utils
 
 from .index import index_sequences
+from .io import open_file, read_sequences, write_sequences
 from .utils import read_metadata, read_strains, get_numerical_dates, run_shell_command, shquote, is_date_ambiguous
 
 comment_char = '#'
@@ -545,19 +546,19 @@ def run(args):
         dropped_samps = list(available_strains - seq_keep)
         write_vcf(args.sequences, args.output, dropped_samps)
     elif args.sequences and args.output:
-        sequences = SeqIO.parse(args.sequences, "fasta")
+        sequences = read_sequences(args.sequences)
 
         # Stream to disk all sequences that passed all filters to avoid reading
         # sequences into memory first. Track the observed strain names in the
         # sequence file as part of the single pass to allow comparison with the
         # provided sequence index.
         observed_sequence_strains = set()
-        with open(args.output, "w") as output_handle:
+        with open_file(args.output, "wt") as output_handle:
             for sequence in sequences:
                 observed_sequence_strains.add(sequence.id)
 
                 if sequence.id in seq_keep:
-                    SeqIO.write(sequence, output_handle, 'fasta')
+                    write_sequences(sequence, output_handle, 'fasta')
 
         if sequence_strains != observed_sequence_strains:
             # Warn the user if the expected strains from the sequence index are