add rna_alignment/rna_align_fetch_cm.py rna_align_fetch_seed.py

rna_tools/tools/rna_alignment/rna_align_fetch_cm.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+
+"""
+from __future__ import print_function
+import argparse
+from icecream import ic
+import sys
+ic.configureOutput(outputFunction=lambda *a: print(*a, file=sys.stderr))
+ic.configureOutput(prefix='> ')
+import requests
+
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    #parser.add_argument('-', "--", help="", default="")
+
+    parser.add_argument("-v", "--verbose",
+                        action="store_true", help="be verbose")
+    parser.add_argument("family", help="", default="", nargs='+')
+    return parser
+
+
+if __name__ == '__main__':
+    parser = get_parser()
+    args = parser.parse_args()
+
+    if list != type(args.family):
+        args.family = [args.family]
+
+    for family in args.family:
+
+            # URL of the Rfam seed alignment
+            url = f"https://rfam.org/family/{family}/cm"
+
+            # Output file name
+            output_file = f"{family}.cm"
+
+            # Download the file
+            response = requests.get(url)
+            if response.status_code == 200:
+                with open(output_file, "wb") as f:
+                    f.write(response.content)
+                print(f"Downloaded model saved as {output_file}")
+            else:
+                print(f"Failed to download. Status code: {response.status_code}")

rna_tools/tools/rna_alignment/rna_align_fetch_seed.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+
+"""
+from __future__ import print_function
+import argparse
+from icecream import ic
+import sys
+ic.configureOutput(outputFunction=lambda *a: print(*a, file=sys.stderr))
+ic.configureOutput(prefix='> ')
+import requests
+
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    #parser.add_argument('-', "--", help="", default="")
+
+    parser.add_argument("-v", "--verbose",
+                        action="store_true", help="be verbose")
+    parser.add_argument("family", help="", default="", nargs='+')
+    return parser
+
+
+if __name__ == '__main__':
+    parser = get_parser()
+    args = parser.parse_args()
+
+    if list != type(args.family):
+        args.family = [args.family]
+
+    for family in args.family:
+
+            # URL of the Rfam seed alignment
+            url = f"https://rfam.org/family/{family}/alignment/fastau"
+
+            # Output file name
+            output_file = f"{family}.seed.sto"
+
+            # Download the file
+            response = requests.get(url)
+            if response.status_code == 200:
+                with open(output_file, "wb") as f:
+                    f.write(response.content)
+                print(f"Downloaded seed alignment saved as {output_file}")
+            else:
+                print(f"Failed to download. Status code: {response.status_code}")

setup.py

@@ -83,6 +83,8 @@
              'rna_tools/tools/rna_alignment/rna_align_find_core.py',
              'rna_tools/tools/rna_alignment/rna_align_get_ss_from_stk.py',
              'rna_tools/tools/rna_alignment/rna_align_seq_to_alignment.py',
+             'rna_tools/tools/rna_alignment/rna_align_fetch_seed.py',
+             'rna_tools/tools/rna_alignment/rna_align_fetch_cm.py',             
              'rna_tools/tools/rna_alignment/utils/rna_alignment_get_species.py',
              'rna_tools/tools/rna_alignment/utils/rna_alignment_process_id.py',
              'rna_tools/tools/rna_alignment/utils/rna_alignment_r2r.py',