Replace utils.open_file in mask with io.open_file

Replaces calls to a similar `open_file` function from `utils.py` with
the new function in `io.py`. Updates the functional tests for the mask
module to confirm that compressed VCF inputs work with the old and new
function alike.

augur/mask.py

@@ -10,8 +10,8 @@
 from Bio import SeqIO
 from Bio.Seq import MutableSeq
 
-from .io import read_sequences, write_sequences
-from .utils import run_shell_command, shquote, open_file, is_vcf, load_mask_sites, VALID_NUCLEOTIDES
+from .io import open_file, read_sequences, write_sequences
+from .utils import run_shell_command, shquote, is_vcf, load_mask_sites, VALID_NUCLEOTIDES
 
 def get_chrom_name(vcf_file):
     """Read the CHROM field from the first non-header line of a vcf file.

tests/functional/mask.t

@@ -5,24 +5,24 @@ Integration tests for augur mask.
 
 Try masking a VCF without any specified mask.
 
-  $ ${AUGUR} mask --sequences mask/variants.vcf
+  $ ${AUGUR} mask --sequences mask/variants.vcf.gz
   No masking sites provided. Must include one of --mask, --mask-from-beginning, --mask-from-end, --mask-invalid, or --mask-sites
   [1]
 
 Mask a VCF with a BED file and no specified output file.
 
-  $ cp "mask/variants.vcf" "$TMP/"
+  $ cp "mask/variants.vcf.gz" "$TMP/"
   $ ${AUGUR} mask \
-  >  --sequences "$TMP/variants.vcf" \
+  >  --sequences "$TMP/variants.vcf.gz" \
   >  --mask "mask/mask_variants.bed" > /dev/null
 
-  $ diff -u "mask/masked_variants.vcf" "$TMP/variants.vcf"
-  $ rm -f "$TMP/variants.vcf"
+  $ diff -u "mask/masked_variants.vcf" <(gzip -c -d "$TMP/variants.vcf.gz")
+  $ rm -f "$TMP/variants.vcf.gz"
 
 Mask a VCF with a BED file and a specified output file.
 
   $ ${AUGUR} mask \
-  >  --sequences "mask/variants.vcf" \
+  >  --sequences "mask/variants.vcf.gz" \
   >  --mask "mask/mask_variants.bed" \
   >  --output "$TMP/masked_variants.vcf" > /dev/null
 
@@ -104,4 +104,4 @@ Mask invalid nucleotides
   ATCGNNNN
   $ rm -f "$TMP/masked.fasta"
 
-  $ popd > /dev/null
+  $ popd > /dev/null