Merge branch 'master' of github.com:mmagnus/rna-tools

README.md

@@ -344,7 +344,7 @@ rna-tools loves to be used with parallel (wirte in shell script what you want rn
 
 ## Tools
 
-The (almost) full list of tools can be found here: <https://github.com/mmagnus/rna-tools/blob/master/index-of-tools.md>
+The (almost) full list of tools can be found here: <https://github.com/mmagnus/rna-tools/blob/master/rna-tools-index.csv>
 
 Read more http://rna-tools.readthedocs.io/en/latest/
 

rna_tools/tools/PyMOL4RNA/PyMOL4Spliceosome.py

@@ -450,6 +450,11 @@ def spl2():
     ino()
 
 
+def x():
+    spl_extract()
+    spl_color()
+cmd.extend("x", x)
+
 def _spli():
     """
     # this trick is taken from Rhiju's Das code
@@ -482,3 +487,4 @@ def _spli():
 
     #cmd.extend("spl", spl)
     cmd.extend("spl2", spl2)
+

rna_tools/tools/df/rna_df_concat.py

@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+https://pandas.pydata.org/docs/reference/api/pandas.concat.html
+"""
+from __future__ import print_function
+import argparse
+import pandas as pd
+import argparse
+from icecream import ic
+import sys
+ic.configureOutput(outputFunction=lambda *a: print(*a, file=sys.stderr))
+ic.configureOutput(prefix='> ')
+
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    parser.add_argument("-v", "--verbose",
+                        action="store_true", help="be verbose")
+    parser.add_argument("-o", "--output", help="", default="_merged_.csv")
+    parser.add_argument('--sep', help="default is ,; can be also '\t'", default=",")
+    parser.add_argument("files", help="", default="", nargs='+')
+    return parser
+
+
+if __name__ == '__main__':
+    parser = get_parser()
+    args = parser.parse_args()
+    print(args)
+    files = args.files
+    dfs = []
+    for f in files:
+        df = pd.read_csv(f, delimiter=args.sep)#, index_col=1)#index=False)
+        print(f)
+        print(df)
+        dfs.append(df)
+    merged = pd.concat(dfs)
+    print(merged)
+    print('saved ', args.output)
+    merged.to_csv(args.output, index=False)
+

rna_tools/tools/misc/rna_merge_dfs.py → rna_tools/tools/df/rna_df_merge.py

@@ -22,7 +22,7 @@ def get_parser():
     parser.add_argument("-v", "--verbose",
                         action="store_true", help="be verbose")
     parser.add_argument("--drop-col", help="", default="")
-    parser.add_argument("-o", "--output", help="", default="'_merged.csv'")
+    parser.add_argument("-o", "--output", help="", default="_merged_.csv")
     parser.add_argument("files", help="", default="", nargs='+')
 
     return parser
@@ -42,4 +42,5 @@ def get_parser():
         dfs.append(df)
     dfs = pd.concat(dfs, axis=1)
     print(dfs)
-    dfs.to_csv(args.output)
+    print('saved ', args.output)
+    dfs.to_csv(args.output, index=False)

rna_tools/tools/df/rna_df_merge_on.py

@@ -0,0 +1,41 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+
+"""
+from __future__ import print_function
+import argparse
+import pandas as pd
+import argparse
+from icecream import ic
+import sys
+ic.configureOutput(outputFunction=lambda *a: print(*a, file=sys.stderr))
+ic.configureOutput(prefix='> ')
+
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+    parser.add_argument("-v", "--verbose",
+                        action="store_true", help="be verbose")
+    parser.add_argument("-o", "--output", help="", default="_merged_.csv")
+    parser.add_argument('--sep', help="default is ,; can be also '\t'", default=",")
+    parser.add_argument('mergeon', help="merge on column", default="")
+    parser.add_argument("files", help="", default="", nargs='+')
+    return parser
+
+
+if __name__ == '__main__':
+    parser = get_parser()
+    args = parser.parse_args()
+
+    files = args.files
+    f1 = files.pop()
+    merged = pd.read_csv(f1, delimiter=args.sep)
+    for f in files:
+        dft = pd.read_csv(f, delimiter=args.sep)
+        merged = pd.merge(merged, dft, on=args.mergeon)#, how=args.how, validate=args.validate)
+    print(merged)
+    print('saved ', args.output)
+    merged.to_csv(args.output, index=False)
+

rna_tools/tools/df/test.sh

@@ -0,0 +1,3 @@
+./rna_df_merge.py test_data/*rmsd.csv --drop-col fn -o test_data/rna_df_merge.csv
+./rna_df_merge_on.py fn test_data/min_*  -o test_data/rna_df_merge_on.csv
+./rna_df_concat.py test_data/d3.csv test_data/d8.csv -o test_data/rna_df_concat.py

rna_tools/tools/df/test_data/d3.csv

@@ -0,0 +1,17 @@
+id,seql,fn_x,rasp_all,fn_y,cs,id_y,seq,growth,growthb,growthby,sl,sledge,slexemplary,sle
+1,aua,1x4.pdbA-22a-C-60u-B-52a-rpr.pdb,-1980.52,1x4.pdbA-22a-C-60u-B-52a-rpr.pdb,17.42,11,aua,0.0,0,n,2.19,3.06,2.47,2.47
+2,auc,1x4.pdbA-22a-C-60u-B-52c-rpr.pdb,-1888.62,1x4.pdbA-22a-C-60u-B-52c-rpr.pdb,7.02,12,auc,0.0,0,n,1.91,3.21,2.29,2.29
+3,aug,1x4.pdbA-22a-C-60u-B-52g-rpr.pdb,-2013.48,1x4.pdbA-22a-C-60u-B-52g-rpr.pdb,20.83,9,auG,0.0,0,n,1.55,3.85,1.55,1.55
+4,auu,1x4.pdbA-22a-C-60u-B-52u-rpr.pdb,-1876.82,1x4.pdbA-22a-C-60u-B-52u-rpr.pdb,7.04,10,auu,0.0,0,n,1.41,3.16,2.74,2.74
+5,cca,1x4.pdbA-22c-C-60c-B-52a-rpr.pdb,-1880.76,1x4.pdbA-22c-C-60c-B-52a-rpr.pdb,17.48,15,Cca,0.0,0,n,2.53,3.71,3.6,3.6
+6,ccc,1x4.pdbA-22c-C-60c-B-52c-rpr.pdb,-1794.79,1x4.pdbA-22c-C-60c-B-52c-rpr.pdb,10.56,16,Ccc,0.0,0,n,1.62,3.87,3.82,3.82
+7,ccg,1x4.pdbA-22c-C-60c-B-52g-rpr.pdb,-1908.65,1x4.pdbA-22c-C-60c-B-52g-rpr.pdb,31.36,13,CcG,0.0,0,n,2.31,3.22,2.63,2.63
+8,ccu,1x4.pdbA-22c-C-60c-B-52u-rpr.pdb,-1781.95,1x4.pdbA-22c-C-60c-B-52u-rpr.pdb,10.6,14,Ccu,0.0,0,n,1.99,3.45,4.16,4.16
+9,cga,1x4.pdbA-22c-C-60g-B-52a-rpr.pdb,-2109.44,1x4.pdbA-22c-C-60g-B-52a-rpr.pdb,6.92,3,CGa,0.0,0,n,1.36,2.69,1.99,1.99
+10,cgc,1x4.pdbA-22c-C-60g-B-52c-rpr.pdb,-2017.49,1x4.pdbA-22c-C-60g-B-52c-rpr.pdb,6.97,4,CGc,0.0,0,n,2.02,3.6,2.12,2.12
+11,cgg,1x4.pdbA-22c-C-60g-B-52g-rpr.pdb,-2148.78,1x4.pdbA-22c-C-60g-B-52g-rpr.pdb,6.9,1,CGG,1.0,1,y,1.92,2.63,1.92,1.92
+12,cgu,1x4.pdbA-22c-C-60g-B-52u-rpr.pdb,-2002.48,1x4.pdbA-22c-C-60g-B-52u-rpr.pdb,6.99,2,CGu,1.0,1,y,1.28,3.4,2.79,2.79
+13,cua,1x4.pdbA-22c-C-60u-B-52a-rpr.pdb,-1887.53,1x4.pdbA-22c-C-60u-B-52a-rpr.pdb,17.54,7,Cua,0.0,0,n,2.55,3.81,2.88,2.88
+14,cuc,1x4.pdbA-22c-C-60u-B-52c-rpr.pdb,-1800.01,1x4.pdbA-22c-C-60u-B-52c-rpr.pdb,7.07,8,Cuc,0.0,0,n,2.2,3.17,3.62,3.62
+15,cug,1x4.pdbA-22c-C-60u-B-52g-rpr.pdb,-1919.04,1x4.pdbA-22c-C-60u-B-52g-rpr.pdb,20.98,5,CuG,0.0,0,n,2.44,3.41,3.38,3.38
+16,cuu,1x4.pdbA-22c-C-60u-B-52u-rpr.pdb,-1788.36,1x4.pdbA-22c-C-60u-B-52u-rpr.pdb,7.09,6,Cuu,0.5,1,y,2.02,3.17,3.71,3.71

rna_tools/tools/df/test_data/d8.csv

@@ -0,0 +1,13 @@
+ID,seq,seql,clarnaOnMutants_b,growth,growth2b,growthb,sle,sledge,slexemplary,stdb,instances,contacts,fn_x,cs,fn_y,rasp_all,fn_x,dfire,md,fn_y,mdMeds
+1,GCU,gcu,1,1.0,1,1,0.04,0.04,0.04,1,14,4,_yCs_5MPS.pdb2-21g-6-61c+80u-rpr.pdb,6.8,t1_yCs_5MPS.pdb2-21g-6-61c+80u-rpr.pdb,-2270.75,_yCs_5MPS.pdb2-21g-6-61c+80u-rpr.pdb,-3788.830125,-34106.025,4chains-A-21g-C-61c-D-80u-rpr_mdr.pdb,-34200.74241156787
+2,GCc,gcc,1,1.0,1,1,1.03,1.03,1.03,1,9,4,_yCs_5MPS.pdb2-21g-6-61c+80c-rpr.pdb,6.78,t1_yCs_5MPS.pdb2-21g-6-61c+80c-rpr.pdb,-2282.79,_yCs_5MPS.pdb2-21g-6-61c+80c-rpr.pdb,-3697.916295,-34314.192,4chains-A-21g-C-61c-D-80c-rpr_mdr.pdb,-34285.268283938814
+3,GCa,gca,1,1.0,1,1,1.86,1.86,1.86,1,9,4,_yCs_5MPS.pdb2-21g-6-61c+80a-rpr.pdb,6.73,t1_yCs_5MPS.pdb2-21g-6-61c+80a-rpr.pdb,-2360.04,_yCs_5MPS.pdb2-21g-6-61c+80a-rpr.pdb,-3837.631784,-34141.484,4chains-A-21g-C-61c-D-80a-rpr_mdr.pdb,-34135.35006871415
+4,GCg,gcg,0,0.5,0,1,1.36,1.36,1.36,1,1,4,_yCs_5MPS.pdb2-21g-6-61c+80g-rpr.pdb,13.42,t1_yCs_5MPS.pdb2-21g-6-61c+80g-rpr.pdb,-2377.54,_yCs_5MPS.pdb2-21g-6-61c+80g-rpr.pdb,-3879.032851,-34263.586,4chains-A-21g-C-61c-D-80g-rpr_mdr.pdb,-34270.27067399617
+5,GgU,ggu,0,0.0,0,0,2.97,4.56,2.97,0,0,-1,_yCs_5MPS.pdb2-21g-6-61g+80u-rpr.pdb,13.65,t1_yCs_5MPS.pdb2-21g-6-61g+80u-rpr.pdb,-2370.41,_yCs_5MPS.pdb2-21g-6-61g+80u-rpr.pdb,-3641.649662,-34513.444,4chains-A-21g-C-61g-D-80u-rpr_mdr.pdb,-34357.67208413001
+6,Ggc,ggc,0,0.0,0,0,2.61,4.08,2.61,0,0,-1,_yCs_5MPS.pdb2-21g-6-61g+80c-rpr.pdb,13.61,t1_yCs_5MPS.pdb2-21g-6-61g+80c-rpr.pdb,-2383.98,_yCs_5MPS.pdb2-21g-6-61g+80c-rpr.pdb,-3572.459166,-34411.725,4chains-A-21g-C-61g-D-80c-rpr_mdr.pdb,-34397.00906728012
+7,Gga,gga,0,0.0,0,0,2.51,4.78,2.51,0,0,-1,_yCs_5MPS.pdb2-21g-6-61g+80a-rpr.pdb,13.51,t1_yCs_5MPS.pdb2-21g-6-61g+80a-rpr.pdb,-2462.93,_yCs_5MPS.pdb2-21g-6-61g+80a-rpr.pdb,-3695.787994,-34182.361,4chains-A-21g-C-61g-D-80a-rpr_mdr.pdb,-34299.49472693595
+8,Ggg,ggg,1,0.0,0,0,3.13,10.0,3.13,0,0,-1,_yCs_5MPS.pdb2-21g-6-61g+80g-rpr.pdb,16.84,t1_yCs_5MPS.pdb2-21g-6-61g+80g-rpr.pdb,-2486.28,_yCs_5MPS.pdb2-21g-6-61g+80g-rpr.pdb,-3716.428175,-34393.949,4chains-A-21g-C-61g-D-80g-rpr_mdr.pdb,-34273.241440607075
+9,cgU,cgu,0,0.5,0,1,2.13,3.81,2.13,0,0,-1,_yCs_5MPS.pdb2-21c-6-61g+80u-rpr.pdb,10.2,t1_yCs_5MPS.pdb2-21c-6-61g+80u-rpr.pdb,-2282.07,_yCs_5MPS.pdb2-21c-6-61g+80u-rpr.pdb,-3828.255247,-34147.373,4chains-A-21c-C-61g-D-80u-rpr_mdr.pdb,-34183.88690547323
+10,cgc,cgc,0,1.0,1,1,1.55,4.0,1.55,0,0,-1,_yCs_5MPS.pdb2-21c-6-61g+80c-rpr.pdb,10.17,t1_yCs_5MPS.pdb2-21c-6-61g+80c-rpr.pdb,-2296.0,_yCs_5MPS.pdb2-21c-6-61g+80c-rpr.pdb,-3748.587568,-34267.798,4chains-A-21c-C-61g-D-80c-rpr_mdr.pdb,-34245.87528381931
+11,cga,cga,0,0.5,0,1,1.35,1.35,1.35,1,20,3,_yCs_5MPS.pdb2-21c-6-61g+80a-rpr.pdb,10.1,t1_yCs_5MPS.pdb2-21c-6-61g+80a-rpr.pdb,-2372.53,_yCs_5MPS.pdb2-21c-6-61g+80a-rpr.pdb,-3880.264616,-34136.491,4chains-A-21c-C-61g-D-80a-rpr_mdr.pdb,-34184.05682361376
+12,cgg,cgg,1,0.0,0,0,1.08,1.08,1.08,1,10,4,_yCs_5MPS.pdb2-21c-6-61g+80g-rpr.pdb,13.42,t1_yCs_5MPS.pdb2-21c-6-61g+80g-rpr.pdb,-2395.09,_yCs_5MPS.pdb2-21c-6-61g+80g-rpr.pdb,-3911.366274,-34219.669,4chains-A-21c-C-61g-D-80g-rpr_mdr.pdb,-34278.04209488528

rna_tools/tools/df/test_data/min_2.csv

@@ -0,0 +1,21 @@
+fn,score
+gac-4chains-A-21g-C-61a-D-80c-rpr_mdr.pdb,-34151.69395315487
+gaa-4chains-A-21g-C-61a-D-80a-rpr_mdr.pdb,-34089.02963671128
+cga-4chains-A-21c-C-61g-D-80a-rpr_mdr.pdb,-34253.88757767686
+gau-4chains-A-21g-C-61a-D-80u-rpr_mdr.pdb,-34239.14391132887
+gag-4chains-A-21g-C-61a-D-80g-rpr_mdr.pdb,-34323.098410611856
+cgg-4chains-A-21c-C-61g-D-80g-rpr_mdr.pdb,-34267.22335086042
+cgc-4chains-A-21c-C-61g-D-80c-rpr_mdr.pdb,-34225.64755616635
+cgu-4chains-A-21c-C-61g-D-80u-rpr_mdr.pdb,-34209.77608150095
+gca-4chains-A-21g-C-61c-D-80a-rpr_mdr.pdb,-34042.77455783939
+ggg-4chains-A-21g-C-61g-D-80g-rpr_mdr.pdb,-34494.786687380496
+gcg-4chains-A-21g-C-61c-D-80g-rpr_mdr.pdb,-34279.05413479923
+gcc-4chains-A-21g-C-61c-D-80c-rpr_mdr.pdb,-34304.87422323135
+gga-4chains-A-21g-C-61g-D-80a-rpr_mdr.pdb,-34230.40899856597
+gcu-4chains-A-21g-C-61c-D-80u-rpr_mdr.pdb,-34198.830365678776
+gua-4chains-A-21g-C-61u-D-80a-rpr_mdr.pdb,-34036.68738049713
+ggc-4chains-A-21g-C-61g-D-80c-rpr_mdr.pdb,-34536.2019000956
+gug-4chains-A-21g-C-61u-D-80g-rpr_mdr.pdb,-34086.65078274378
+ggu-4chains-A-21g-C-61g-D-80u-rpr_mdr.pdb,-34375.280084847036
+guu-4chains-A-21g-C-61u-D-80u-rpr_mdr.pdb,-34015.68475143403
+guc-4chains-A-21g-C-61u-D-80c-rpr_mdr.pdb,-34113.29245339388

rna_tools/tools/df/test_data/min_3.csv

@@ -0,0 +1,21 @@
+fn,score
+gau-4chains-A-21g-C-61a-D-80u-rpr_mdr.pdb,-33992.53853967495
+gag-4chains-A-21g-C-61a-D-80g-rpr_mdr.pdb,-34024.65493546845
+cga-4chains-A-21c-C-61g-D-80a-rpr_mdr.pdb,-34064.8377748566
+cgc-4chains-A-21c-C-61g-D-80c-rpr_mdr.pdb,-34205.261113766726
+cgu-4chains-A-21c-C-61g-D-80u-rpr_mdr.pdb,-34065.528650812616
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+gaa-4chains-A-21g-C-61a-D-80a-rpr_mdr.pdb,-34278.18027007648
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+gca-4chains-A-21g-C-61c-D-80a-rpr_mdr.pdb,-34104.88617351816
+gcc-4chains-A-21g-C-61c-D-80c-rpr_mdr.pdb,-34130.41497370937
+gga-4chains-A-21g-C-61g-D-80a-rpr_mdr.pdb,-34465.62051864245
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+gcu-4chains-A-21g-C-61c-D-80u-rpr_mdr.pdb,-34182.2194670172
+ggu-4chains-A-21g-C-61g-D-80u-rpr_mdr.pdb,-34391.38683078394
+guc-4chains-A-21g-C-61u-D-80c-rpr_mdr.pdb,-34129.58592256214
+ggg-4chains-A-21g-C-61g-D-80g-rpr_mdr.pdb,-34421.92728250478
+ggc-4chains-A-21g-C-61g-D-80c-rpr_mdr.pdb,-34392.43621534417
+gua-4chains-A-21g-C-61u-D-80a-rpr_mdr.pdb,-33999.443564770554
+gug-4chains-A-21g-C-61u-D-80g-rpr_mdr.pdb,-34187.007050669214
+guu-4chains-A-21g-C-61u-D-80u-rpr_mdr.pdb,-34022.36197418738

rna_tools/tools/df/test_data/min_4.csv

@@ -0,0 +1,21 @@
+fn,score
+cga-4chains-A-21c-C-61g-D-80a-rpr_mdr.pdb,-34190.14026649139
+cgg-4chains-A-21c-C-61g-D-80g-rpr_mdr.pdb,-34301.71113169216
+gaa-4chains-A-21g-C-61a-D-80a-rpr_mdr.pdb,-34189.51287643403
+gag-4chains-A-21g-C-61a-D-80g-rpr_mdr.pdb,-34067.758126195025
+cgc-4chains-A-21c-C-61g-D-80c-rpr_mdr.pdb,-34280.167005258125
+gac-4chains-A-21g-C-61a-D-80c-rpr_mdr.pdb,-34238.08332337476
+cgu-4chains-A-21c-C-61g-D-80u-rpr_mdr.pdb,-34184.36304971319
+gau-4chains-A-21g-C-61a-D-80u-rpr_mdr.pdb,-34058.40702676864
+gca-4chains-A-21g-C-61c-D-80a-rpr_mdr.pdb,-34153.617202437854
+ggg-4chains-A-21g-C-61g-D-80g-rpr_mdr.pdb,-34252.44980879541
+gcg-4chains-A-21g-C-61c-D-80g-rpr_mdr.pdb,-34276.79851816443
+gcc-4chains-A-21g-C-61c-D-80c-rpr_mdr.pdb,-34251.788808556405
+gga-4chains-A-21g-C-61g-D-80a-rpr_mdr.pdb,-34052.93977055449
+guc-4chains-A-21g-C-61u-D-80c-rpr_mdr.pdb,-34103.98243307839
+gcu-4chains-A-21g-C-61c-D-80u-rpr_mdr.pdb,-34125.97096080306
+ggc-4chains-A-21g-C-61g-D-80c-rpr_mdr.pdb,-34404.33421964627
+ggu-4chains-A-21g-C-61g-D-80u-rpr_mdr.pdb,-34218.38028800191
+gug-4chains-A-21g-C-61u-D-80g-rpr_mdr.pdb,-34144.81506931166
+gua-4chains-A-21g-C-61u-D-80a-rpr_mdr.pdb,-34111.39161089866
+guu-4chains-A-21g-C-61u-D-80u-rpr_mdr.pdb,-34098.642148661565

rna_tools/tools/df/test_data/rna_df_concat.py

@@ -0,0 +1,29 @@
+id,seql,fn_x,rasp_all,fn_y,cs,id_y,seq,growth,growthb,growthby,sl,sledge,slexemplary,sle,ID,clarnaOnMutants_b,growth2b,stdb,instances,contacts,fn_x.1,dfire,md,fn_y.1,mdMeds
+1.0,aua,1x4.pdbA-22a-C-60u-B-52a-rpr.pdb,-1980.52,1x4.pdbA-22a-C-60u-B-52a-rpr.pdb,17.42,11.0,aua,0.0,0,n,2.19,3.06,2.47,2.47,,,,,,,,,,,
+2.0,auc,1x4.pdbA-22a-C-60u-B-52c-rpr.pdb,-1888.62,1x4.pdbA-22a-C-60u-B-52c-rpr.pdb,7.02,12.0,auc,0.0,0,n,1.91,3.21,2.29,2.29,,,,,,,,,,,
+3.0,aug,1x4.pdbA-22a-C-60u-B-52g-rpr.pdb,-2013.48,1x4.pdbA-22a-C-60u-B-52g-rpr.pdb,20.83,9.0,auG,0.0,0,n,1.55,3.85,1.55,1.55,,,,,,,,,,,
+4.0,auu,1x4.pdbA-22a-C-60u-B-52u-rpr.pdb,-1876.82,1x4.pdbA-22a-C-60u-B-52u-rpr.pdb,7.04,10.0,auu,0.0,0,n,1.41,3.16,2.74,2.74,,,,,,,,,,,
+5.0,cca,1x4.pdbA-22c-C-60c-B-52a-rpr.pdb,-1880.76,1x4.pdbA-22c-C-60c-B-52a-rpr.pdb,17.48,15.0,Cca,0.0,0,n,2.53,3.71,3.6,3.6,,,,,,,,,,,
+6.0,ccc,1x4.pdbA-22c-C-60c-B-52c-rpr.pdb,-1794.79,1x4.pdbA-22c-C-60c-B-52c-rpr.pdb,10.56,16.0,Ccc,0.0,0,n,1.62,3.87,3.82,3.82,,,,,,,,,,,
+7.0,ccg,1x4.pdbA-22c-C-60c-B-52g-rpr.pdb,-1908.65,1x4.pdbA-22c-C-60c-B-52g-rpr.pdb,31.36,13.0,CcG,0.0,0,n,2.31,3.22,2.63,2.63,,,,,,,,,,,
+8.0,ccu,1x4.pdbA-22c-C-60c-B-52u-rpr.pdb,-1781.95,1x4.pdbA-22c-C-60c-B-52u-rpr.pdb,10.6,14.0,Ccu,0.0,0,n,1.99,3.45,4.16,4.16,,,,,,,,,,,
+9.0,cga,1x4.pdbA-22c-C-60g-B-52a-rpr.pdb,-2109.44,1x4.pdbA-22c-C-60g-B-52a-rpr.pdb,6.92,3.0,CGa,0.0,0,n,1.36,2.69,1.99,1.99,,,,,,,,,,,
+10.0,cgc,1x4.pdbA-22c-C-60g-B-52c-rpr.pdb,-2017.49,1x4.pdbA-22c-C-60g-B-52c-rpr.pdb,6.97,4.0,CGc,0.0,0,n,2.02,3.6,2.12,2.12,,,,,,,,,,,
+11.0,cgg,1x4.pdbA-22c-C-60g-B-52g-rpr.pdb,-2148.78,1x4.pdbA-22c-C-60g-B-52g-rpr.pdb,6.9,1.0,CGG,1.0,1,y,1.92,2.63,1.92,1.92,,,,,,,,,,,
+12.0,cgu,1x4.pdbA-22c-C-60g-B-52u-rpr.pdb,-2002.48,1x4.pdbA-22c-C-60g-B-52u-rpr.pdb,6.99,2.0,CGu,1.0,1,y,1.28,3.4,2.79,2.79,,,,,,,,,,,
+13.0,cua,1x4.pdbA-22c-C-60u-B-52a-rpr.pdb,-1887.53,1x4.pdbA-22c-C-60u-B-52a-rpr.pdb,17.54,7.0,Cua,0.0,0,n,2.55,3.81,2.88,2.88,,,,,,,,,,,
+14.0,cuc,1x4.pdbA-22c-C-60u-B-52c-rpr.pdb,-1800.01,1x4.pdbA-22c-C-60u-B-52c-rpr.pdb,7.07,8.0,Cuc,0.0,0,n,2.2,3.17,3.62,3.62,,,,,,,,,,,
+15.0,cug,1x4.pdbA-22c-C-60u-B-52g-rpr.pdb,-1919.04,1x4.pdbA-22c-C-60u-B-52g-rpr.pdb,20.98,5.0,CuG,0.0,0,n,2.44,3.41,3.38,3.38,,,,,,,,,,,
+16.0,cuu,1x4.pdbA-22c-C-60u-B-52u-rpr.pdb,-1788.36,1x4.pdbA-22c-C-60u-B-52u-rpr.pdb,7.09,6.0,Cuu,0.5,1,y,2.02,3.17,3.71,3.71,,,,,,,,,,,
+,gcu,_yCs_5MPS.pdb2-21g-6-61c+80u-rpr.pdb,-2270.75,t1_yCs_5MPS.pdb2-21g-6-61c+80u-rpr.pdb,6.8,,GCU,1.0,1,,,0.04,0.04,0.04,1.0,1.0,1.0,1.0,14.0,4.0,_yCs_5MPS.pdb2-21g-6-61c+80u-rpr.pdb,-3788.830125,-34106.025,4chains-A-21g-C-61c-D-80u-rpr_mdr.pdb,-34200.74241156787
+,gcc,_yCs_5MPS.pdb2-21g-6-61c+80c-rpr.pdb,-2282.79,t1_yCs_5MPS.pdb2-21g-6-61c+80c-rpr.pdb,6.78,,GCc,1.0,1,,,1.03,1.03,1.03,2.0,1.0,1.0,1.0,9.0,4.0,_yCs_5MPS.pdb2-21g-6-61c+80c-rpr.pdb,-3697.916295,-34314.192,4chains-A-21g-C-61c-D-80c-rpr_mdr.pdb,-34285.268283938814
+,gca,_yCs_5MPS.pdb2-21g-6-61c+80a-rpr.pdb,-2360.04,t1_yCs_5MPS.pdb2-21g-6-61c+80a-rpr.pdb,6.73,,GCa,1.0,1,,,1.86,1.86,1.86,3.0,1.0,1.0,1.0,9.0,4.0,_yCs_5MPS.pdb2-21g-6-61c+80a-rpr.pdb,-3837.631784,-34141.484,4chains-A-21g-C-61c-D-80a-rpr_mdr.pdb,-34135.35006871415
+,gcg,_yCs_5MPS.pdb2-21g-6-61c+80g-rpr.pdb,-2377.54,t1_yCs_5MPS.pdb2-21g-6-61c+80g-rpr.pdb,13.42,,GCg,0.5,1,,,1.36,1.36,1.36,4.0,0.0,0.0,1.0,1.0,4.0,_yCs_5MPS.pdb2-21g-6-61c+80g-rpr.pdb,-3879.032851,-34263.586,4chains-A-21g-C-61c-D-80g-rpr_mdr.pdb,-34270.27067399617
+,ggu,_yCs_5MPS.pdb2-21g-6-61g+80u-rpr.pdb,-2370.41,t1_yCs_5MPS.pdb2-21g-6-61g+80u-rpr.pdb,13.65,,GgU,0.0,0,,,4.56,2.97,2.97,5.0,0.0,0.0,0.0,0.0,-1.0,_yCs_5MPS.pdb2-21g-6-61g+80u-rpr.pdb,-3641.649662,-34513.444,4chains-A-21g-C-61g-D-80u-rpr_mdr.pdb,-34357.67208413001
+,ggc,_yCs_5MPS.pdb2-21g-6-61g+80c-rpr.pdb,-2383.98,t1_yCs_5MPS.pdb2-21g-6-61g+80c-rpr.pdb,13.61,,Ggc,0.0,0,,,4.08,2.61,2.61,6.0,0.0,0.0,0.0,0.0,-1.0,_yCs_5MPS.pdb2-21g-6-61g+80c-rpr.pdb,-3572.459166,-34411.725,4chains-A-21g-C-61g-D-80c-rpr_mdr.pdb,-34397.00906728012
+,gga,_yCs_5MPS.pdb2-21g-6-61g+80a-rpr.pdb,-2462.93,t1_yCs_5MPS.pdb2-21g-6-61g+80a-rpr.pdb,13.51,,Gga,0.0,0,,,4.78,2.51,2.51,7.0,0.0,0.0,0.0,0.0,-1.0,_yCs_5MPS.pdb2-21g-6-61g+80a-rpr.pdb,-3695.787994,-34182.361,4chains-A-21g-C-61g-D-80a-rpr_mdr.pdb,-34299.49472693595
+,ggg,_yCs_5MPS.pdb2-21g-6-61g+80g-rpr.pdb,-2486.28,t1_yCs_5MPS.pdb2-21g-6-61g+80g-rpr.pdb,16.84,,Ggg,0.0,0,,,10.0,3.13,3.13,8.0,1.0,0.0,0.0,0.0,-1.0,_yCs_5MPS.pdb2-21g-6-61g+80g-rpr.pdb,-3716.428175,-34393.949,4chains-A-21g-C-61g-D-80g-rpr_mdr.pdb,-34273.241440607075
+,cgu,_yCs_5MPS.pdb2-21c-6-61g+80u-rpr.pdb,-2282.07,t1_yCs_5MPS.pdb2-21c-6-61g+80u-rpr.pdb,10.2,,cgU,0.5,1,,,3.81,2.13,2.13,9.0,0.0,0.0,0.0,0.0,-1.0,_yCs_5MPS.pdb2-21c-6-61g+80u-rpr.pdb,-3828.255247,-34147.373,4chains-A-21c-C-61g-D-80u-rpr_mdr.pdb,-34183.88690547323
+,cgc,_yCs_5MPS.pdb2-21c-6-61g+80c-rpr.pdb,-2296.0,t1_yCs_5MPS.pdb2-21c-6-61g+80c-rpr.pdb,10.17,,cgc,1.0,1,,,4.0,1.55,1.55,10.0,0.0,1.0,0.0,0.0,-1.0,_yCs_5MPS.pdb2-21c-6-61g+80c-rpr.pdb,-3748.587568,-34267.798,4chains-A-21c-C-61g-D-80c-rpr_mdr.pdb,-34245.87528381931
+,cga,_yCs_5MPS.pdb2-21c-6-61g+80a-rpr.pdb,-2372.53,t1_yCs_5MPS.pdb2-21c-6-61g+80a-rpr.pdb,10.1,,cga,0.5,1,,,1.35,1.35,1.35,11.0,0.0,0.0,1.0,20.0,3.0,_yCs_5MPS.pdb2-21c-6-61g+80a-rpr.pdb,-3880.264616,-34136.491,4chains-A-21c-C-61g-D-80a-rpr_mdr.pdb,-34184.05682361376
+,cgg,_yCs_5MPS.pdb2-21c-6-61g+80g-rpr.pdb,-2395.09,t1_yCs_5MPS.pdb2-21c-6-61g+80g-rpr.pdb,13.42,,cgg,0.0,0,,,1.08,1.08,1.08,12.0,1.0,0.0,1.0,10.0,4.0,_yCs_5MPS.pdb2-21c-6-61g+80g-rpr.pdb,-3911.366274,-34219.669,4chains-A-21c-C-61g-D-80g-rpr_mdr.pdb,-34278.04209488528

rna_tools/tools/df/test_data/rna_df_merge.csv

@@ -0,0 +1,10 @@
+cga,cgc
+1.53,1.5
+1.53,1.45
+1.54,1.41
+1.57,1.43
+1.59,1.43
+1.58,1.51
+1.56,1.54
+1.56,1.52
+1.52,1.45