feat: added code to filter plasmids from chromosomes

1 files changed, 43 insertions, 0 deletions

diff --git a/scripts/filter_plasmids.py b/scripts/filter_plasmids.py
new file mode 100755
index 0000000..9461451
--- /dev/null
+++ b/scripts/filter_plasmids.py
@@ -0,0 +1,43 @@
+#!/usr/bin/env python3
+"""
+script to filter plasmids and chromosomes from full genome assemblies
+"""
+
+import os
+import sys
+import gzip
+import builtins
+
+from glob import glob
+
+sys.path.insert(0, os.path.abspath('.')) # gross hack
+from pangraph.utils import parse_fasta, breakpoint
+
+from Bio import SeqIO
+
+def open(path, *args, **kwargs):
+    if path.endswith('.gz'):
+        return gzip.open(path, *args, **kwargs)
+    else:
+        return builtins.open(path, *args, **kwargs)
+
+# def main(args):
+#     for d in args:
+
+from time import time
+if __name__ == "__main__":
+    t0 = time()
+    for path in glob("data/staph/assemblies/*.fna.gz"):
+        with open(path, 'rt') as fd:
+            seqs = [record for record in SeqIO.parse(fd, 'fasta')]
+    t1 = time()
+    print(f"bio parser took {t1 - t0} seconds")
+
+    t0 = time()
+    for path in glob("data/staph/assemblies/*.fna.gz"):
+        with open(path, 'rt') as fd:
+            seqs = [record for record in parse_fasta(fd)]
+    t1 = time()
+    print(f"my parser took {t1 - t0} seconds")
+
+    # main(sys.argv[1:])