reinstate setup.py

core/jms-implementation/support-mini-x86-32/setup.py

@@ -0,0 +1,102 @@
+#!/usr/bin/env python3
+
+import argparse
+import glob
+import os
+import subprocess as sp
+import sys
+
+
+PROPERTIES="interproscan.properties"
+
+
+def load_properties(file, properties):
+    with open(file, "rt") as fh:
+        for line in map(str.strip, fh):
+            if not line or line[0] == "#":
+                continue
+
+            fields = line.split("=", 1)
+            if len(fields) == 2:
+                key = fields[0].strip()
+                value = fields[1].strip()
+                properties[key] = value
+
+    try:
+        bin_dir = properties["bin.directory"]
+        data_dir = properties["data.directory"]
+    except KeyError:
+        return
+
+    for key, value in properties.items():
+        if "${bin.directory}" in value:
+            value = value.replace("${bin.directory}", bin_dir)
+
+        if "${data.directory}" in value:
+            value = value.replace("${data.directory}", data_dir)
+
+        properties[key] = value
+
+
+def is_ready(hmmfile):
+    for ext in [".h3m", ".h3i", ".h3f", ".h3p"]:
+        if not os.path.isfile(hmmfile + ext):
+            return False
+
+    return True
+
+
+def hmmpress(binary, force, database):
+    if force:
+        cmd = [binary, "-f", database]
+    else:
+        cmd = [binary, database]
+
+    proc = sp.Popen(cmd, stdout=sp.PIPE, stderr=sp.PIPE)
+    outs, errs = proc.communicate()
+
+    if proc.returncode != 0:
+        sys.stderr.write(errs.decode())
+        sys.exit(1)
+
+
+def realpath(path):
+    return os.path.realpath(os.path.expanduser(path))
+
+
+def main():
+    parser = argparse.ArgumentParser(description="index HMM databases")
+    parser.add_argument("properties", help="InterProScan properties file")
+    parser.add_argument("-f", "--force", action="store_true",
+                        help="re-index all HMM databases (default: off)")
+    args = parser.parse_args()
+
+    properties = {}
+    load_properties(PROPERTIES, properties)
+
+    if realpath(args.properties) != realpath(PROPERTIES):
+        load_properties(args.properties, properties)
+
+    ignore = {"binary.tmhmm.path", "funfam.hmm.path", "smart.hmm.path"}
+    for key, path in properties.items():
+        if "hmm.path" in key and key not in ignore:
+            bin_key = "binary.hmmer3.path"
+
+            if os.path.isfile(path):
+                hmmfiles = [path]
+            else:
+                hmmfiles = glob.iglob(os.path.join(path, "**", "*.hmm"),
+                                      recursive=True)
+
+            for hmmfile in hmmfiles:
+                if args.force or not is_ready(hmmfile):
+                    try:
+                        bin_path = os.path.join(properties[bin_key], "hmmpress")
+                    except KeyError:
+                        continue
+                    else:
+                        hmmpress(bin_path, args.force, hmmfile)
+
+
+if __name__ == '__main__':
+    main()