RNApolis 0.4.8__py3-none-any.whl → 0.4.10__py3-none-any.whl

{RNApolis-0.4.8.dist-info → RNApolis-0.4.10.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.4.8
+Version: 0.4.10
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

RNApolis-0.4.10.dist-info/RECORD

@@ -0,0 +1,17 @@
+rnapolis/annotator.py,sha256=_hsSX2VHFvIQ47l_EA7lwGFXLiVLbhFPEsOQzBKbjRk,22100
+rnapolis/clashfinder.py,sha256=i95kp0o6OWNqmJDBr-PbsZd7RY2iJtBDr7QqolJSuAQ,8513
+rnapolis/common.py,sha256=LY6Uz96Br8ki_gA8LpfatgtvVbt9jOTkwgagayqTgf8,31251
+rnapolis/metareader.py,sha256=I1-cXc2YNBPwa3zihAnMTjEsAo79tEKzSmWu5yvN1Pk,2071
+rnapolis/molecule_filter.py,sha256=hB6-nXgjmw7FAsQ3bj0cZ2FvuW2I1PXunEfcdwEUB1o,7389
+rnapolis/motif_extractor.py,sha256=Lfn1iEkhkP9eZD3GPEWNAfy00QO7QPCc8wM_XS1ory8,1147
+rnapolis/parser.py,sha256=2pQYy0sh8TCpeluMmmSJ7C5dudK_bsfstTWCdpwwpNU,15193
+rnapolis/rfam_folder.py,sha256=SjiiyML_T1__saruFwSMJEoQ7Y55GIU8ktS8ZUn5-fw,11111
+rnapolis/tertiary.py,sha256=6t9ZB4w33-5n_M3sns1RoFXCOTgVAgGH4WDNG5OG9Kg,23426
+rnapolis/transformer.py,sha256=V9nOQvdq4-p7yUWo0vQg0CDQMpmyxz9t4TMSRVEKHnw,1817
+rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
+RNApolis-0.4.10.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
+RNApolis-0.4.10.dist-info/METADATA,sha256=AiTwfWTRaaJ_Zd_E1UIYMu54Hi0vu9WN8dYA67x3SLk,54323
+RNApolis-0.4.10.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+RNApolis-0.4.10.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
+RNApolis-0.4.10.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
+RNApolis-0.4.10.dist-info/RECORD,,

rnapolis/annotator.py

@@ -9,6 +9,7 @@ from typing import Dict, List, Optional, Set, Tuple
 
 import numpy
 import numpy.typing
+import orjson
 from ordered_set import OrderedSet
 from rnapolis.common import (
     BR,

rnapolis/common.py

@@ -940,6 +940,27 @@ class BpSeq:
             solutions.add(self.__make_dot_bracket(regions, orders))
         return list(solutions)
 
+    def without_pseudoknots(self):
+        return BpSeq.from_dotbracket(self.dot_bracket.without_pseudoknots())
+
+    def without_isolated(self):
+        stems, _, _, _ = self.elements
+        to_unpair = []
+
+        for stem in stems:
+            if stem.strand5p.first == stem.strand5p.last:
+                to_unpair.append(stem.strand5p.first - 1)
+                to_unpair.append(stem.strand3p.first - 1)
+
+        if not to_unpair:
+            return self
+
+        entries = self.entries.copy()
+        for i in to_unpair:
+            entries[i].pair = 0
+
+        return BpSeq(entries)
+
 
 @dataclass
 class DotBracket:
@@ -990,6 +1011,10 @@ class DotBracket:
     def __hash__(self) -> int:
         return hash((self.sequence, self.structure))
 
+    def without_pseudoknots(self):
+        structure = re.sub(r"[\[\]\{\}\<\>A-Za-z]", ".", self.structure)
+        return DotBracket(self.sequence, structure)
+
 
 @dataclass
 class MultiStrandDotBracket(DotBracket):

rnapolis/motif_extractor.py

@@ -9,6 +9,12 @@ def main():
     parser = argparse.ArgumentParser()
     parser.add_argument("--dbn", help="path to DotBracket file")
     parser.add_argument("--bpseq", help="path to BpSeq file")
+    parser.add_argument(
+        "--remove-pseudoknots", action="store_true", help="remove pseudoknots"
+    )
+    parser.add_argument(
+        "--remove-isolated", action="store_true", help="remove isolated base pairs"
+    )
     args = parser.parse_args()
 
     if args.dbn:
@@ -19,6 +25,12 @@ def main():
         parser.print_help()
         return
 
+    if args.remove_isolated:
+        bpseq = bpseq.without_isolated()
+
+    if args.remove_pseudoknots:
+        bpseq = bpseq.without_pseudoknots()
+
     print(f"Full dot-bracket:\n{bpseq.dot_bracket}")
     stems, single_strands, hairpins, loops = bpseq.elements
 

RNApolis-0.4.8.dist-info/RECORD

@@ -1,17 +0,0 @@
-rnapolis/annotator.py,sha256=7U3f0gchKdIGc6FwJx0UAc_95HJI5SgECj-b7-1yBhc,22086
-rnapolis/clashfinder.py,sha256=i95kp0o6OWNqmJDBr-PbsZd7RY2iJtBDr7QqolJSuAQ,8513
-rnapolis/common.py,sha256=7KSWZzqR7ntpaS6VRDYgpP2pC1dnBttOzYB06hQzWEI,30499
-rnapolis/metareader.py,sha256=I1-cXc2YNBPwa3zihAnMTjEsAo79tEKzSmWu5yvN1Pk,2071
-rnapolis/molecule_filter.py,sha256=hB6-nXgjmw7FAsQ3bj0cZ2FvuW2I1PXunEfcdwEUB1o,7389
-rnapolis/motif_extractor.py,sha256=duHvpi9Ulcny9K60E6VBpz5RpJZw-KdTB4_Ph0iP478,774
-rnapolis/parser.py,sha256=2pQYy0sh8TCpeluMmmSJ7C5dudK_bsfstTWCdpwwpNU,15193
-rnapolis/rfam_folder.py,sha256=SjiiyML_T1__saruFwSMJEoQ7Y55GIU8ktS8ZUn5-fw,11111
-rnapolis/tertiary.py,sha256=6t9ZB4w33-5n_M3sns1RoFXCOTgVAgGH4WDNG5OG9Kg,23426
-rnapolis/transformer.py,sha256=V9nOQvdq4-p7yUWo0vQg0CDQMpmyxz9t4TMSRVEKHnw,1817
-rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
-RNApolis-0.4.8.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-RNApolis-0.4.8.dist-info/METADATA,sha256=FZsizaaGYKRz7ndlAySWt8mPfpjjHUoP-OzXaO3LBv8,54322
-RNApolis-0.4.8.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-RNApolis-0.4.8.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
-RNApolis-0.4.8.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-RNApolis-0.4.8.dist-info/RECORD,,