diff extract_data_for_profrep.py @ 0:a5f1638b73be draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_data_for_profrep.py	Wed Jun 26 08:01:42 2019 -0400
@@ -0,0 +1,62 @@
+#!/usr/bin/env python3
+
+import zipfile
+import tempfile
+import argparse
+from shutil import copyfile
+import os
+import configuration
+
+
+def main(args):
+
+    RE_ARCHIVE = args.re_archive
+    OUTPUT_CLS = args.output_cls
+    OUTPUT_READS_ALL = args.output_reads_all
+    OUTPUT_ANNOTATION = args.output_annotation
+
+    if not os.path.isabs(OUTPUT_CLS):
+        OUTPUT_CLS = os.path.join(os.getcwd(), OUTPUT_CLS)
+
+    if not os.path.isabs(OUTPUT_READS_ALL):
+        OUTPUt_READS_ALL = os.path.join(os.getcwd(), OUTPUT_READS_ALL)
+
+    if not os.path.isabs(OUTPUT_ANNOTATION):
+        OUTPUT_ANNOTATION = os.path.join(os.getcwd(), OUTPUT_ANNOTATION)
+
+    with tempfile.TemporaryDirectory() as dirpath:
+        with zipfile.ZipFile(RE_ARCHIVE, 'r') as re_archive:
+            re_archive.extractall(dirpath)
+        copyfile(os.path.join(dirpath, configuration.HITSORT_CLS), OUTPUT_CLS)
+        copyfile(
+            os.path.join(dirpath, configuration.READS_ALL), OUTPUT_READS_ALL)
+        copyfile(
+            os.path.join(dirpath, configuration.ANNOTATION), OUTPUT_ANNOTATION)
+
+
+if __name__ == '__main__':
+
+    # Command line arguments
+    parser = argparse.ArgumentParser()
+    parser.add_argument('-ar',
+                        '--re_archive',
+                        type=str,
+                        required=True,
+                        help='RepeatExplorer output data archive')
+    parser.add_argument('-oc',
+                        '--output_cls',
+                        type=str,
+                        default="output_hitsort_cls",
+                        help='Output cls file of all clusters')
+    parser.add_argument('-or',
+                        '--output_reads_all',
+                        type=str,
+                        default="output_reads_all",
+                        help='Output file of all reads sequences')
+    parser.add_argument('-oa',
+                        '--output_annotation',
+                        type=str,
+                        default="output_annotation",
+                        help='Output file of clusters annotation')
+    args = parser.parse_args()
+    main(args)