v1.8.0 - Add II-C2, II-D, and V-M

pentamorfico · Dec 16, 2022 · 99719a1 · 99719a1
1 parent 2e8c6ac
commit 99719a1
Show file tree

Hide file tree

Showing 8 changed files with 719 additions and 710 deletions.
diff --git a/data/CasScoring.csv b/data/CasScoring.csv
diff --git a/data/Profiles.tar.gz b/data/Profiles.tar.gz
diff --git a/data/adaptation.json b/data/adaptation.json
@@ -25,6 +25,10 @@
          ["Cas4"]],
 "II-C": [["Cas1_"], 
          ["Cas2"]],
+"II-C2": [["Cas1_"], 
+         ["Cas2"]],
+"II-D": [["Cas1_"], 
+         ["Cas2"]],
 "V-A": [["Cas1_"], 
         ["Cas2"], 
         ["Cas4"]],

diff --git a/data/cutoffs.tab b/data/cutoffs.tab
@@ -7,7 +7,6 @@ cas12e:1e-10,0.6,0.25
 cas12f1:1e-70,0.75,0.75
 cas12f2:1e-100,0.7,0.7
 cas12f3:1e-100,0.8,0.8
-cas12f4:1e-50,0.7,0.7
 cas12f6:1e-10,0.7,0.7
 cas12f7:1e-10,0.7,0.7
 cas12g:1e-10,0.6,0.25
@@ -16,6 +15,7 @@ cas12i:1e-5,0.9,0.25
 cas12j:1e-10,0.6,0.25
 cas12k:1e-5,0.9,0.25
 cas12l:1e-10,0.6,0.25
+cas12m:1e-50,0.7,0.7
 cas13a:1e-10,0.05,0.55
 cas13b:1e-10,0.95,0.85
 cas13c:1e-10,0.9,0.75

diff --git a/data/interference.json b/data/interference.json
@@ -43,6 +43,8 @@
 "II-A": [["Cas9"]],
 "II-B": [["Cas9"]],
 "II-C": [["Cas9"]],
+"II-C2": [["Cas9"]],
+"II-D": [["Cas9"]],
 "III-A": [["Cas10"], 
           ["Csm2"], 
           ["Csm3"], 
@@ -122,6 +124,7 @@
         ["TnsB"], 
         ["TnsC"]],
 "V-L": [["Cas12"]],
+"V-M": [["Cas12"]],
 "VI-A": [["Cas13"]],
 "VI-B1": [["Cas13"]],
 "VI-B2": [["Cas13"]],

diff --git a/data/type_dict.tab b/data/type_dict.tab
@@ -23,11 +23,11 @@ IV-E:21
 V-A:22
 V-B1:23
 V-E:24
-V-F:25
-V-F1:26
-V-F2:27
-V-F3:28
-V-G:29
+V-F1:25
+V-F2:26
+V-F3:27
+V-G:28
+V-I:29
 V-J:30
 V-K:31
 VI-A:32

diff --git a/data/xgb_repeats.model b/data/xgb_repeats.model
diff --git a/setup.py b/setup.py
@@ -5,14 +5,14 @@
 
 setuptools.setup(
     name="cctyper", 
-    version="1.7.1",
+    version="1.8.0",
     author="Jakob Russel",
     author_email="[email protected]",
     description="CRISPRCasTyper: Automatic detection and subtyping of CRISPR-Cas operons",
     long_description=long_description,
     long_description_content_type="text/markdown",
     url="https://github.com/Russel88/CRISPRCasTyper",
-    download_url="https://github.com/Russel88/CRISPRCasTyper/archive/v1.7.1.tar.gz",
+    download_url="https://github.com/Russel88/CRISPRCasTyper/archive/v1.8.0.tar.gz",
     packages=setuptools.find_packages(),
     classifiers=[
         "Programming Language :: Python :: 3",
-Original file line number
+Diff line change
@@ Expand Up / @@ -23,11 +23,11 @@ IV-E:21 @@
     V-A:22
     V-B1:23
     V-E:24
-    V-F:25
-    V-F1:26
-    V-F2:27
-    V-F3:28
-    V-G:29
+    V-F1:25
+    V-F2:26
+    V-F3:27
+    V-G:28
+    V-I:29
     V-J:30
     V-K:31
     VI-A:32
@@ Expand Down @@