Port to pysam >= 0.14

snakecnv/bin/findNstretches.py

@@ -7,7 +7,7 @@ import re
 import multiprocessing
 from functools import partial
 
-from pysam import Fastafile
+from pysam import FastaFile
 
 
 def eprint(*args, **kwargs):
@@ -15,14 +15,14 @@ def eprint(*args, **kwargs):
 
 
 def get_chromosomes(fastafile):
-    with Fastafile(fastafile) as fasta:
+    with FastaFile(fastafile) as fasta:
         chromosomes = fasta.references
     return chromosomes
 
 
 def find_chrom_Nstretches(chrom, fastafile, cutoff):
     p = re.compile("N{%s,}" % cutoff)
-    with Fastafile(fastafile) as fasta:
+    with FastaFile(fastafile) as fasta:
         sequence = fasta.fetch(chrom)
         gaps = [(chrom, m.start(), m.end() + 1) for m in re.finditer(p, sequence)]
     return gaps