Fix #40 deprecate fileinput usage in fasta

morrislab · Oct 23, 2020 · 86d7201 · 86d7201
1 parent c7ea04c
commit 86d7201
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Showing 2 changed files with 2 additions and 3 deletions.
diff --git a/qapa/fasta.py b/qapa/fasta.py
@@ -1,4 +1,3 @@
-import fileinput
 import sys
 from Bio import SeqIO
 import pybedtools
@@ -18,7 +17,7 @@ def filter_sequences(fasta_file, min_length=100, fout=sys.stdout):
     seqs = set()
     ids = set()
     skipped = 0
-    handle = fileinput.input(fasta_file)
+    handle = open(fasta_file, 'r')
 
     for record in SeqIO.parse(handle, "fasta"):
         sequence = str(record.seq)

diff --git a/setup.py b/setup.py
@@ -23,7 +23,7 @@
       install_requires=['setuptools',
                         'pandas >= 0.24',
                         'numpy >= 1.10.0',
-                        'biopython >= 1.66',
+                        'biopython >= 1.76',
                         'pybedtools >= 0.7.9'
                         ],
       entry_points={