initial commit

README.md

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+## command to get file sizes
+
+```
+find . -type f -printf "%k %p\n" | tee ~/scratch/magsearch/ls-wort.txt
+```

scripts/intersect-ls-and-catalog.py

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+#! /usr/bin/env python
+import argparse
+import sys
+import os.path
+
+
+def main():
+    p = argparse.ArgumentParser()
+    p.add_argument('filesize_output')
+    p.add_argument('catalog')
+    args = p.parse_args()
+
+    metagenomes = set()
+    with open(args.catalog, 'rt') as fp:
+        for line in fp:
+            acc = os.path.basename(line.strip())
+            acc = os.path.splitext(acc)[0]
+            metagenomes.add(acc)
+    print(f"loaded {len(metagenomes)} accessions from '{args.catalog}'",
+          file=sys.stderr)
+    print(f"example acc: {next(iter(metagenomes))}", file=sys.stderr)
+
+    acc_sizes = {}
+    with open(args.filesize_output, 'rt') as fp:
+        for line in fp:
+            size, filename = line.strip().split(' ', 1)
+            acc = os.path.basename(filename)
+            acc = os.path.splitext(acc)[0]
+
+            if acc in metagenomes:
+                size = int(size)
+                acc_sizes[acc] = size
+
+    print(f"Loaded {len(acc_sizes)} file sizes from '{args.filesize_output}'")
+
+    if len(metagenomes) != len(acc_sizes):
+        print(f"WARNING: missing some filesizes for some accessions.",
+              file=sys.stderr)
+
+    avg = sum(acc_sizes.values()) / len(acc_sizes)
+    print(f"average file size: {avg:.1f}")
+
+    sizes = list(acc_sizes.values())
+    sizes.sort()
+    median = sizes[len(sizes) // 2]
+    print(f"median file size: {median}")
+
+
+if __name__ == '__main__':
+    sys.exit(main())