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

* 'master' of github.com:mmagnus/rna-tools:
  Add files via upload

rna_tools/tools/automatix/README.md

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+# automatix
+xx or makex
+
+```
+[mm] evox$ git:(master) ✗ xxdownload_job_and_process.py ade ade_cp15-ca11f0d6
+mkdir: simrna_ade_cp15-ca11f0d6: File exists
+/usr/local/lib/python2.7/site-packages/urllib3/connectionpool.py:858: InsecureRequestWarning: Unverified HTTPS request is being made. Adding certificate verification is strongly advised. See: https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings
+  InsecureRequestWarning)
+['ade_cp15', 'ca11f0d6', 'thrs6.50A_clust04X.
+```

rna_tools/tools/automatix/after_peyote_clean.sh

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+yes | rm *.e4*
+yes | rm *.o4*
+yes | rm *.po*
+yes | rm *.o4*
+yes | rm *.pe*

rna_tools/tools/automatix/automatix.py

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+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+/home/magnus/rna-evo-malibu/ade # run here not up
+"""
+from __future__ import print_function
+
+import argparse
+import os
+import glob
+
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    parser.add_argument('-d', "--dryrun",
+                        action="store_true", help="dry run", default=False)
+
+    parser.add_argument('-p', '--path', help="", default='')
+    parser.add_argument('-c', '--case', help="only one case, for test", default="*")
+    parser.add_argument('-e', '--exe', help="only one case, for test")
+    parser.add_argument("-v", "--verbose",
+                        action="store_true", help="be verbose")
+    return parser
+
+def exe(cmd, dryrun=False):
+    print(cmd)
+    if not dryrun: os.system(cmd)
+
+if __name__ == '__main__':
+    parser = get_parser()
+    args = parser.parse_args()
+
+    if args.path:
+        os.chdir(args.path)
+    root = os.getcwd()
+    cases = glob.glob(args.case)# '*')
+    for c in cases:
+        print('Case: ', c)
+        # mode only for a specific case
+        #if args.case: # only if this is used
+        #     if c != args.case:
+        #        print('!!! skip ' + c + '!!!')
+        #        continue
+
+        # if not break ed, use this
+        if os.path.isdir(c):
+            print ('Inside %s' % c)
+            os.chdir(c) # go inside a folder
+            if args.exe:
+                exe(args.exe)
+            #subcases = glob.glob('*.fa')
+            #for sc in subcases:
+            ## for i in [1000]: #
+            ##     exe('rm *min.out.*.pdb', dryrun)
+            ##     exe('mkdir %s_top%i' % (c, i), dryrun)
+            ##     exe('extract_lowscore_decoys.py *min.out %i' % (i), dryrun)
+            ##     exe('mv -v *min.out.*.pdb %s_top%i' % (c, i), dryrun)
+            ## os.chdir(root)

rna_tools/tools/automatix/chunker.py

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+
+
+
+def chunks(l, n):
+    """Yield successive n-sized chunks from l."""
+    for i in range(0, len(l), n):
+        yield l[i:i + n]
+
+#main
+f = open('pdb_list.txt').read().split()
+# 30 = runs * 10 = 300cores
+no_of_files = int(round(len(f) / 100))
+c = 0
+for i in chunks(f, no_of_files):
+    txt = "echo '" 
+    # -g farna_hires.csv
+    txt += "/home/magnus/mqaprna_env/mqapRNA/main/mqaprna  -o FARNA__hires_" + str(c) + " " + " ".join(i) +"'"
+    txt += " | qsub -N mq" + str(c) + " -V -cwd -pe mpi 1"
+    print txt
+    c += 1
+

rna_tools/tools/automatix/clean.sh

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+yes | rm *.e4*
+yes | rm *.o4*
+yes | rm *.po*
+yes | rm *.o4*
+yes | rm *.pe*

rna_tools/tools/automatix/evox.py

@@ -0,0 +1,62 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+/home/magnus/rna-evo-malibu/ade # run here not up
+"""
+from __future__ import print_function
+
+import argparse
+import os
+import glob
+
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    parser.add_argument('-d', "--dryrun",
+                        action="store_true", help="dry run", default=False)
+
+    parser.add_argument('-p', '--path', help="", default='')
+    parser.add_argument('-c', '--case', help="only one case, for test")
+    parser.add_argument("-v", "--verbose",
+                        action="store_true", help="be verbose")
+
+    return parser
+
+def exe(cmd, dryrun):
+    print(cmd)
+    if not dryrun: os.system(cmd)
+
+def main(dryrun, path, case):
+    if path:
+        os.chdir(path)
+    root = os.getcwd()
+    cases = glob.glob('*')
+    for c in cases:
+        print('Case: ', c)
+        # mode only for a specific case
+        if case: # only if this is used
+            if c != case:
+                print('!!! skip ' + c + '!!!')
+                continue
+
+        # if not break ed, use this
+        if os.path.isdir(c):
+            print ('Inside %s' % c)
+            os.chdir(c) # go inside a folder
+            # cmd
+            #subcases = glob.glob('*.fa')
+            #for sc in subcases:
+            for i in [1000]: #
+                exe('rm *min.out.*.pdb', dryrun)
+                exe('mkdir %s_top%i' % (c, i), dryrun)
+                exe('extract_lowscore_decoys.py *min.out %i' % (i), dryrun)
+                exe('mv -v *min.out.*.pdb %s_top%i' % (c, i), dryrun)
+            os.chdir(root)
+
+if __name__ == '__main__':
+    parser = get_parser()
+    args = parser.parse_args()
+
+    main(args.dryrun, args.path, args.case)

rna_tools/tools/automatix/inf_all.py

@@ -0,0 +1,17 @@
+#!/usr/bin/env python
+import os
+import glob
+
+def main():
+    root = os.getcwd()
+    pdbs = glob.glob('*')
+    for p in pdbs:
+        if os.path.isdir(p):
+            os.chdir(p) # go inside a folder
+            cmd = 'rna_calc_inf.py -t struc/' + p + '_M1.pdb struc/*.pdb'
+            print cmd
+            os.system(cmd)
+            os.chdir(root)
+
+if __name__ == '__main__':
+    main()

rna_tools/tools/automatix/mass_inf.py

@@ -0,0 +1,17 @@
+#!/usr/bin/env python
+import os
+import glob
+
+def main():
+    root = os.getcwd()
+    pdbs = glob.glob('*')
+    for p in pdbs:
+        if os.path.isdir(p):
+            os.chdir(p) # go inside a folder
+            cmd = 'rna_calc_inf.py -t struc/' + p + '_M1.pdb struc/*.pdb'
+            print cmd
+            #os.system
+            os.chdir(root)
+
+if __name__ == '__main__':
+    main()

rna_tools/tools/automatix/mqaprna_massive_destruction.py

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+#!/usr/bin/python
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+1 - method
+2 - cpu
+3 - "_X.csv' (without csv
+
+   print "1 - method, 2 - cpu, 3 - '_X.csv' (without csv) 4 - run 5 - method_code, e.g. Fhi"
+"""
+from __future__ import print_function
+
+import argparse
+import sys
+import os
+import glob
+
+
+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("method")
+    parser.add_argument("cpu", type=int)
+    parser.add_argument("--run", action="store_true") # nargs='+')
+    parser.add_argument("path")
+    parser.add_argument("--subfolder", default="struc", help="struc in this case /home/mqapRNA/mqaprna_datasets/rasp/2nueC/struc/2nueC_M10.pdb")
+    parser.add_argument("dirs", nargs='+')# help="", default="") # 
+    return parser
+
+
+if __name__ == '__main__':
+    parser = get_parser()
+    args = parser.parse_args()
+
+    missing = ''
+
+    files = os.listdir(PATH)
+    method = args.method
+    cpu = int(args.cpu)
+    method_code = ''#sys.argv[5]
+
+    for f in args.dirs:
+        if os.path.isdir(f):
+            print('#' * 80)
+            print(f)
+            if missing:
+                if f not in  missing.split(','):
+                    continue
+
+            #cmd = 'cp -v ' + f + '/' + f + '.pdb ' + f + '/struc/'
+            #print cmd
+            #cmd = "mqaprna.py -n 1a9nR/1a9nR.pdb 1a9nR/struc/ 1a9nR"
+            #cmd = "mqaprna.py -m 6 -t SimRNA_1 " + f + '/struc ' + f + '_simrna_1_'
+
+            #cmd = "mqaprna.py -m " + str(cpu) + " -g /home/magnus/mqaprna_decoys/rasp/" + f + '_' + method + "-v0.3-48-g80cbfc0-dirty.csv -t " + method + "  " + PATH + f + '/struc ' + PATH + '_' + f + '_' + method 
+
+            pattern = path + '/*' + f + '*' + method + '**csv'
+            print(pattern)
+            csvfn_to_ignore = glob.glob(pattern)
+            print(csvfn_to_ignore)
+            if len(csvfn_to_ignore) > 0:
+                g = " -g " + csvfn_to_ignore[0]
+            else:
+                print('nothing to ignore...')
+                g = ''
+            #g = '' # g hack!
+
+            if cpu > 0:
+                multi_cpu = ' -m ' + str(cpu)
+                cpu_c = cpu
+            else:
+                multi_cpu = ''
+                cpu_c = '1'
+
+            cmd = "mqaprna.py " + multi_cpu + " "  + g + " -t " + method + "  " + PATH + f + os.sep + args.subfolder + '/*.pdb -o ' + PATH + '' + f + '_' + method
+            print(cmd)
+
+            #cmd2 = 'echo "' + cmd + '" | qsub -cwd -V -pe mpi ' + str(cpu_c) + '  -N _' + f + method_code #+ f + '_'+method #  -l h_vmem=300M -l mem_free=500M
+            # print cmd2
+            #RASP,SimRNA,AnalyzeGeometry,FARNA,QRNA,NAST_pyro,radiu
+            #                s_of_gyration,SSAgreement,ClashScore,RNAkb
+            if args.run:
+                os.system(cmd)
+

rna_tools/tools/automatix/pdb_list.txt

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+3f1hB/struc/3f1hB_M204.pdb 3f1hB/struc/3f1hB_M425.pdb 3f1hB/struc/3f1hB_M404.pdb 3f1hB/struc/3f1hB_M330.pdb 3f1hB/struc/3f1hB_M57.pdb 3f1hB/struc/3f1hB_M337.pdb 3f1hB/struc/3f1hB_M217.pdb 3f1hB/struc/3f1hB_M213.pdb 3f1hB/struc/3f1hB_M141.pdb 3f1hB/struc/3f1hB_M380.pdb 3f1hB/struc/3f1hB_M143.pdb 3f1hB/struc/3f1hB_M465.pdb 3f1hB/struc/3f1hB_M48.pdb 3f1hB/struc/3f1hB_M78.pdb 3f1hB/struc/3f1hB_M500.pdb 3f1hB/struc/3f1hB_M450.pdb 3f1hB/struc/3f1hB_M384.pdb 3f1hB/struc/3f1hB_M16.pdb 3f1hB/struc/3f1hB_M403.pdb 3f1hB/struc/3f1hB_M198.pdb 3f1hB/struc/3f1hB_M87.pdb 3f1hB/struc/3f1hB_M287.pdb 3f1hB/struc/3f1hB_M463.pdb 3f1hB/struc/3f1hB_M372.pdb 3f1hB/struc/3f1hB_M304.pdb 3f1hB/struc/3f1hB_M441.pdb 3f1hB/struc/3f1hB_M260.pdb 3f1hB/struc/3f1hB_M432.pdb 3f1hB/struc/3f1hB_M180.pdb 3f1hB/struc/3f1hB_M378.pdb 3f1hB/struc/3f1hB_M274.pdb 3f1hB/struc/3f1hB_M479.pdb 3f1hB/struc/3f1hB_M70.pdb 3f1hB/struc/3f1hB_M438.pdb 3f1hB/struc/3f1hB_M245.pdb 3f1hB/struc/3f1hB_M448.pdb 3f1hB/struc/3f1hB_M409.pdb 3f1hB/struc/3f1hB_M12.pdb 3f1hB/struc/3f1hB_M151.pdb 3f1hB/struc/3f1hB_M110.pdb 3f1hB/struc/3f1hB_M185.pdb 3f1hB/struc/3f1hB_M257.pdb 3f1hB/struc/3f1hB_M435.pdb 3f1hB/struc/3f1hB_M246.pdb 3f1hB/struc/3f1hB_M219.pdb 3f1hB/struc/3f1hB_M81.pdb 3f1hB/struc/3f1hB_M208.pdb 3f1hB/struc/3f1hB_M389.pdb 3f1hB/struc/3f1hB_M363.pdb 3f1hB/struc/3f1hB_M440.pdb 3f1hB/struc/3f1hB_M117.pdb 3f1hB/struc/3f1hB_M63.pdb 3f1hB/struc/3f1hB_M2.pdb 3f1hB/struc/3f1hB_M360.pdb 3f1hB/struc/3f1hB_M431.pdb 3f1hB/struc/3f1hB_M452.pdb 3f1hB/struc/3f1hB_M353.pdb 3f1hB/struc/3f1hB_M224.pdb 3f1hB/struc/3f1hB_M340.pdb 3f1hB/struc/3f1hB_M135.pdb 3f1hB/struc/3f1hB_M228.pdb 3f1hB/struc/3f1hB_M174.pdb 3f1hB/struc/3f1hB_M152.pdb 3f1hB/struc/3f1hB_M216.pdb 3f1hB/struc/3f1hB_M49.pdb 3f1hB/struc/3f1hB_M284.pdb 3f1hB/struc/3f1hB_M273.pdb 3f1hB/struc/3f1hB_M328.pdb 3f1hB/struc/3f1hB_M475.pdb 3f1hB/struc/3f1hB_M104.pdb 3f1hB/struc/3f1hB_M53.pdb 3f1hB/struc/3f1hB_M227.pdb 3f1hB/struc/3f1hB_M173.pdb 3f1hB/struc/3f1hB_M329.pdb 3f1hB/struc/3f1hB_M58.pdb 3f1hB/struc/3f1hB_M83.pdb 3f1hB/struc/3f1hB_M7.pdb 3f1hB/struc/3f1hB_M418.pdb 3f1hB/struc/3f1hB_M331.pdb 3f1hB/struc/3f1hB_M415.pdb 3f1hB/struc/3f1hB_M39.pdb 3f1hB/struc/3f1hB_M60.pdb 3f1hB/struc/3f1hB_M412.pdb 3f1hB/struc/3f1hB_M9.pdb 3f1hB/struc/3f1hB_M458.pdb 3f1hB/struc/3f1hB_M294.pdb 3f1hB/struc/3f1hB_M453.pdb 3f1hB/struc/3f1hB_M168.pdb 3f1hB/struc/3f1hB_M147.pdb 3f1hB/struc/3f1hB_M237.pdb 3f1hB/struc/3f1hB_M207.pdb 3f1hB/struc/3f1hB_M390.pdb 3f1hB/struc/3f1hB_M232.pdb 3f1hB/struc/3f1hB_M200.pdb 3f1hB/struc/3f1hB_M126.pdb 3f1hB/struc/3f1hB_M121.pdb 3f1hB/struc/3f1hB_M343.pdb 3f1hB/struc/3f1hB_M408.pdb 3f1hB/struc/3f1hB_M93.pdb 3f1hB/struc/3f1hB_M221.pdb 3f1hB/struc/3f1hB_M347.pdb 3f1hB/struc/3f1hB_M206.pdb 3f1hB/struc/3f1hB_M280.pdb 3f1hB/struc/3f1hB_M146.pdb 3f1hB/struc/3f1hB_M128.pdb 3f1hB/struc/3f1hB_M267.pdb 3f1hB/struc/3f1hB_M188.pdb 3f1hB/struc/3f1hB_M398.pdb 3f1hB/struc/3f1hB_M103.pdb 3f1hB/struc/3f1hB_M97.pdb 3f1hB/struc/3f1hB_M332.pdb 3f1hB/struc/3f1hB_M222.pdb 3f1hB/struc/3f1hB_M410.pdb 3f1hB/struc/3f1hB_M249.pdb 3f1hB/struc/3f1hB_M113.pdb 3f1hB/struc/3f1hB_M424.pdb 3f1hB/struc/3f1hB_M88.pdb 3f1hB/struc/3f1hB_M127.pdb 3f1hB/struc/3f1hB_M120.pdb 3f1hB/struc/3f1hB_M129.pdb 3f1hB/struc/3f1hB_M239.pdb 3f1hB/struc/3f1hB_M29.pdb 3f1hB/struc/3f1hB_M32.pdb 3f1hB/struc/3f1hB_M169.pdb 3f1hB/struc/3f1hB_M405.pdb 3f1hB/struc/3f1hB_M381.pdb 3f1hB/struc/3f1hB_M47.pdb 3f1hB/struc/3f1hB_M84.pdb 3f1hB/struc/3f1hB_M350.pdb 3f1hB/struc/3f1hB_M262.pdb 3f1hB/struc/3f1hB_M357.pdb 3f1hB/struc/3f1hB_M489.pdb 3f1hB/struc/3f1hB_M485.pdb 3f1hB/struc/3f1hB_M191.pdb 3f1hB/struc/3f1hB_M429.pdb 3f1hB/struc/3f1hB_M44.pdb 3f1hB/struc/3f1hB_M189.pdb 3f1hB/struc/3f1hB_M85.pdb 3f1hB/struc/3f1hB_M125.pdb 3f1hB/struc/3f1hB_M20.pdb 3f1hB/struc/3f1hB_M214.pdb 3f1hB/struc/3f1hB_M5.pdb 3f1hB/struc/3f1hB_M278.pdb 3f1hB/struc/3f1hB_M469.pdb 3f1hB/struc/3f1hB_M355.pdb 3f1hB/struc/3f1hB_M478.pdb 3f1hB/struc/3f1hB_M321.pdb 3f1hB/struc/3f1hB_M323.pdb 3f1hB/struc/3f1hB_M423.pdb 3f1hB/struc/3f1hB_M183.pdb 3f1hB/struc/3f1hB_M165.pdb 3f1hB/struc/3f1hB_M449.pdb 3f1hB/struc/3f1hB_M96.pdb 3f1hB/struc/3f1hB_M244.pdb 3f1hB/struc/3f1hB_M307.pdb 3f1hB/struc/3f1hB_M211.pdb 3f1hB/struc/3f1hB_M266.pdb 3f1hB/struc/3f1hB_M496.pdb 3f1hB/struc/3f1hB_M338.pdb 3f1hB/struc/3f1hB_M349.pdb 3f1hB/struc/3f1hB_M133.pdb 3f1hB/struc/3f1hB_M498.pdb 3f1hB/struc/3f1hB_M252.pdb 3f1hB/struc/3f1hB_M137.pdb 3f1hB/struc/3f1hB_M250.pdb 3f1hB/struc/3f1hB_M140.pdb 3f1hB/struc/3f1hB_M215.pdb 3f1hB/struc/3f1hB_M172.pdb 3f1hB/struc/3f1hB_M112.pdb 3f1hB/struc/3f1hB_M290.pdb 3f1hB/struc/3f1hB_M40.pdb 3f1hB/struc/3f1hB_M41.pdb 3f1hB/struc/3f1hB_M36.pdb 3f1hB/struc/3f1hB_M43.pdb 3f1hB/struc/3f1hB_M354.pdb 3f1hB/struc/3f1hB_M317.pdb 3f1hB/struc/3f1hB_M383.pdb 3f1hB/struc/3f1hB_M263.pdb 3f1hB/struc/3f1hB_M437.pdb 3f1hB/struc/3f1hB_M241.pdb 3f1hB/struc/3f1hB_M495.pdb 3f1hB/struc/3f1hB_M138.pdb 3f1hB/struc/3f1hB_M171.pdb 3f1hB/struc/3f1hB_M359.pdb 3f1hB/struc/3f1hB_M226.pdb 3f1hB/struc/3f1hB_M130.pdb 3f1hB/struc/3f1hB_M300.pdb 3f1hB/struc/3f1hB_M92.pdb 3f1hB/struc/3f1hB_M167.pdb 3f1hB/struc/3f1hB_M361.pdb 3f1hB/struc/3f1hB_M46.pdb 3f1hB/struc/3f1hB_M101.pdb 3f1hB/struc/3f1hB_M480.pdb 3f1hB/struc/3f1hB_M474.pdb 3f1hB/struc/3f1hB_M160.pdb 3f1hB/struc/3f1hB_M392.pdb 3f1hB/struc/3f1hB_M439.pdb 3f1hB/struc/3f1hB_M35.pdb 3f1hB/struc/3f1hB_M72.pdb 3f1hB/struc/3f1hB_M301.pdb 3f1hB/struc/3f1hB_M385.pdb 3f1hB/struc/3f1hB_M24.pdb 3f1hB/struc/3f1hB_M417.pdb 3f1hB/struc/3f1hB_M377.pdb 3f1hB/struc/3f1hB_M358.pdb 3f1hB/struc/3f1hB_M111.pdb 3f1hB/struc/3f1hB_M352.pdb 3f1hB/struc/3f1hB_M277.pdb 3f1hB/struc/3f1hB_M25.pdb 3f1hB/struc/3f1hB_M282.pdb 3f1hB/struc/3f1hB_M132.pdb 3f1hB/struc/3f1hB_M443.pdb 3f1hB/struc/3f1hB_M163.pdb 3f1hB/struc/3f1hB_M145.pdb 3f1hB/struc/3f1hB_M270.pdb 3f1hB/struc/3f1hB_M445.pdb 3f1hB/struc/3f1hB_M394.pdb 3f1hB/struc/3f1hB_M155.pdb 3f1hB/struc/3f1hB_M460.pdb 3f1hB/struc/3f1hB_M316.pdb 3f1hB/struc/3f1hB_M324.pdb 3f1hB/struc/3f1hB_M238.pdb 3f1hB/struc/3f1hB_M364.pdb 3f1hB/struc/3f1hB_M86.pdb 3f1hB/struc/3f1hB_M65.pdb 3f1hB/struc/3f1hB_M447.pdb 3f1hB/struc/3f1hB_M422.pdb 3f1hB/struc/3f1hB_M258.pdb

rna_tools/tools/automatix/rm_csvs_smaller_than_2k.sh

@@ -0,0 +1 @@
+find -name "*.csv" -size -2k

rna_tools/tools/automatix/rm_less_2k.sh

@@ -0,0 +1 @@
+find -name "*.csv" -size -2k

rna_tools/tools/automatix/rp13_automatix.py

@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+"""
+/home/magnus/rna-evo-malibu/ade # run here not up
+"""
+from __future__ import print_function
+
+import argparse
+import os
+import glob
+
+
+def get_parser():
+    parser = argparse.ArgumentParser(
+        description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter)
+
+    parser.add_argument('-d', "--dryrun",
+                        action="store_true", help="dry run", default=False)
+
+    parser.add_argument('-p', '--path', help="", default='')
+    parser.add_argument('-c', '--case', help="only one case, for test")
+    parser.add_argument('-e', '--exe', help="only one case, for test")
+    parser.add_argument("-v", "--verbose",
+                        action="store_true", help="be verbose")
+    return parser
+
+def exe(cmd, dryrun=False):
+    print(cmd)
+    if not dryrun: os.system(cmd)
+
+if __name__ == '__main__':
+    parser = get_parser()
+    args = parser.parse_args()
+
+    if args.path:
+        os.chdir(args.path)
+    root = os.getcwd()
+    cases = glob.glob('*')
+    for c in cases:
+        # print('Case: ', c)
+        # mode only for a specific case
+        os.chdir(root)  # change to run and go to another case
+        if args.case: # only if this is used
+            if c != args.case:
+                if args.verbose: print('!!! skip ' + c + '!!!')
+                continue
+
+        # if not break ed, use this
+        if os.path.isdir(c):
+            print ('Inside %s' % c)
+            os.chdir(c) # go inside a folder
+            if args.exe:
+                exe(args.exe)
+            #subcases = glob.glob('*.fa')
+            #for sc in subcases:
+            ## for i in [1000]: #
+            ##     exe('rm *min.out.*.pdb', dryrun)
+            ##     exe('mkdir %s_top%i' % (c, i), dryrun)
+            ##     exe('extract_lowscore_decoys.py *min.out %i' % (i), dryrun)
+            ##     exe('mv -v *min.out.*.pdb %s_top%i' % (c, i), dryrun)
+            ## os.chdir(root)
+            malibu_folder = c.replace('_cst', 'cst').replace('farna_', '')
+            print(c, malibu_folder)
+            # exe('trash top100')
+            exe('mkdir top100')
+            exe('pwd')
+            os.chdir('top100')  # cd top100 didn't work ?!
+            exe('rsync -v malibu:"~/rna-evo-malibu/_rp13_Stanford/_reg_vs_cst/%s/*.pdb" . ' %  malibu_folder)
+            exe('rm c.*pdb')
+            exe('rm *out.1[0-9][1-9]*.pdb')
+            exe('rm *out.1[1-9]0*.pdb')
+            exe('rm *out.200.pdb')
+            exe('rm p[0-9].pdb')
+            exe('rna_pdb_toolsx.py --rpr --renumber_residues --inplace  *')
+            os.chdir('..')
+            exe('evox.py -c rp13')