Merge pull request #71 from KULL-Centre/issue67

software/rosetta_ddG_pipeline/args_pipeline.py

@@ -143,7 +143,7 @@ def parse_args2():
     parser.add_argument('--mp_calc_span_mode',
                         choices=['False', 'deepTMHMM', 'struc', 'DSSP', 'octopus',
                                  'bcl', 'Boctopus'],
-                        default='DSSP',
+                        default='deepTMHMM',
                         dest='MP_CALC_SPAN_MODE',
                         help=('Function/mode to calculate the membrane spanning region/file:\n'
                               '\tFalse: file will not be calculated \n'
@@ -152,7 +152,7 @@ def parse_args2():
                               '\toctopus: uses octopus \n'
                               '\tbcl: should be used for helix & beta sheets \n'
                               '\tBoctopus: should be used for beta sheets \n'
-                              'Default value: DSSP'
+                              'Default value: deepTMHMM'
                               )
                         )
     parser.add_argument('--mp_align_ref',
@@ -164,13 +164,14 @@ def parse_args2():
                               )
                         )
     parser.add_argument('--mp_prep_align_mode',
-                        choices=['False', 'OPM', 'PDBTM',
+                        choices=['False', 'OPM', 'span', 'PDBTM',
                                  'TMDET', 'MemProtMD'],
                         default='OPM',
                         dest='MP_ALIGN_MODE',
                         help=('Function/mode to align the membrane protein structure:\n'
                               '\tFalse: structure will not be rearranged \n'
                               '\tOPM: uses the information provided in OPM \n'
+                              '\tspan: positiones the structure based on the information in span file \n'
                               '\tPDBTM: uses the information provided in PDBTM (better than OPM but not tested) \n'
                               '\tTMDET: uses the information provided in TMDET \n'
                               '\tMemProtMD: uses the information provided in MemProtMD \n'
@@ -362,8 +363,12 @@ def parse_args2():
         if (args.MP_ALIGN_MODE=='OPM') and (args.MP_ALIGN_REF == '-'):
             parser.error('Please specify a reference PDBid and chain for alginment into membrane plane or switch "MP_ALIGN_MODE" to false')
             sys.exit()
-        if args.MP_ALIGN_REF != '-':
-            args.MP_ALIGN_MODE='OPM'
+        if args.MP_CALC_SPAN_MODE == 'deepTMHMM':
+            args.MP_ALIGN_MODE = 'span'
+            args.MP_ALIGN_REF = '-'
+        else:
+            if args.MP_ALIGN_REF != '-':
+                args.MP_ALIGN_MODE='OPM'
         if args.MP_CART_DDG == 1:
             args.RELAX_XML_INPUT = os.path.join(rosetta_paths.path_to_data, 'mp', 'mp_cart_relax.xml')
         if args.MP_SPAN_INPUT != None:

software/rosetta_ddG_pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/ddg_flagfile

@@ -0,0 +1,12 @@
+-fa_max_dis 9.0
+-ddg::dump_pdbs false
+-ddg:iterations 3
+-score:weights beta_nov16_cart
+-missing_density_to_jump
+-ddg:mut_only
+-ddg:bbnbrs 1
+-beta_cart
+-ex1
+-ex2
+-ddg::legacy true
+-optimize_proline true

software/rosetta_ddG_pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/mutfiles/mutfile00010

@@ -0,0 +1,5 @@
+total 2
+1
+M 10 M
+1
+M 10 A

software/rosetta_ddG_pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/mutfiles/mutfile00100

@@ -0,0 +1,5 @@
+total 2
+1
+Q 100 Q
+1
+Q 100 A

software/rosetta_ddG_pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/mutfiles/mutfile111_164

@@ -0,0 +1,7 @@
+total 4
+2
+S 111 S
+H 164 H
+2
+S 111 A
+H 164 A

software/rosetta_ddG_pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/parse_ddgs.sbatch

@@ -0,0 +1,9 @@
+#!/bin/sh 
+#SBATCH --job-name=6xro_final_renum_p-ddg
+#SBATCH --array=1 
+#SBATCH --nodes=1 
+#SBATCH --time=0:10:00 
+#SBATCH --partition=sbinlab 
+
+#This sbatch script launches the parse parse_rosetta_ddgs function, from the parse_cartesian_ddgs 
+python3XXXtagvXXX1

software/rosetta_ddG_pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/rosetta_ddg.sbatch

@@ -0,0 +1,18 @@
+#!/bin/sh 
+#SBATCH --job-name=6xro_final_renum_MPcartddg
+#SBATCH --array=0-2
+#SBATCH --time=48:00:00
+#SBATCH --mem 2000
+#SBATCH --partition=sbinlab
+#SBATCH --nice 
+LST=(`ls /ddG/input/mutfiles/mutfile*`)
+OFFSET=0 
+INDEX=$((OFFSET+SLURM_ARRAY_TASK_ID))
+echo $INDEX
+
+# launching rosetta 
+if test -f "/ddG/input/input.pdb"; then
+	bin/cartesian_ddg. -database  -s /ddG/input/input.pdb -ddg:mut_file ${LST[$INDEX]} -score:weights /data/mp/f19_cart_1.5.wts -mp:lipids:composition DLPC -ddg:iterations 5 -ddg::dump_pdbs 0 -mp:setup:spanfiles /ddG/input/spanfiles/input_A_A.span -in:membrane -fa_max_dis 9 -missing_density_to_jump -has_pore 0 -ddg:legacy true -ddg:optimize_proline 1 -ddg:frag_nbrs 4 -ddg:bbnbrs 1 -ddg::cartesian -out:prefix ddg-$SLURM_ARRAY_JOB_ID-$SLURM_ARRAY_TASK_ID 
+else
+	echo "/ddG/input/input.pdb does not exist - exiting the call"
+fi

software/rosetta_ddG_pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/spanfiles/A/TMRs.gff3

@@ -0,0 +1,16 @@
+##gff-version 3
+# input Length: 182
+# input Number of predicted TMRs: 6
+input	inside	1	5				
+input	TMhelix	6	24				
+input	outside	25	51				
+input	TMhelix	52	72				
+input	inside	73	78				
+input	TMhelix	79	99				
+input	outside	100	101				
+input	TMhelix	102	122				
+input	inside	123	132				
+input	TMhelix	133	155				
+input	outside	156	159				
+input	TMhelix	160	180				
+input	inside	181	182				

software/rosetta_ddG_pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/spanfiles/A/deeptmhmm_results.md

@@ -0,0 +1,32 @@
+## DeepTMHMM - Predictions
+Predicted topologies can be downloaded in [.gff3 format](TMRs.gff3) and [.3line format](predicted_topologies.3line)
+![picture](plot.png)
+You can download the probabilities used to generate this plot [here](input_probs.csv)
+### Predicted Topologies
+```
+>input | TM
+ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA
+IIIIIMMMMMMMMMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMMMMMMMIIIIIIMMMMMMMMMMMMMMMMMMMMMOOMMMMMMMMMMMMMMMMMMMMMIIIIIIIIIIMMMMMMMMMMMMMMMMMMMMMMMOOOOMMMMMMMMMMMMMMMMMMMMMII
+
+```
+
+
+```
+##gff-version 3
+# input Length: 182
+# input Number of predicted TMRs: 6
+input	inside	1	5				
+input	TMhelix	6	24				
+input	outside	25	51				
+input	TMhelix	52	72				
+input	inside	73	78				
+input	TMhelix	79	99				
+input	outside	100	101				
+input	TMhelix	102	122				
+input	inside	123	132				
+input	TMhelix	133	155				
+input	outside	156	159				
+input	TMhelix	160	180				
+input	inside	181	182				
+
+```

software/rosetta_ddG_pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/spanfiles/A/input_probs.csv

@@ -0,0 +1,184 @@
+# input
+#AA,Beta,Periplasm,Membrane,Inside,Outside,Signal
+0 E,0.0,0.0,0.0,0.99942,0.00023,0.0
+1 R,0.0,0.0,0.00018,0.99921,0.00023,0.0
+2 A,0.0,0.0,0.01323,0.98618,0.00019,0.0
+3 G,0.0,0.0,0.10431,0.89527,2e-05,0.0
+4 P,0.0,0.0,0.47862,0.52095,0.0,0.0
+5 V,0.0,0.0,0.85568,0.14391,0.0,0.0
+6 T,0.0,0.0,0.90611,0.09348,0.0,0.0
+7 W,0.0,0.0,0.98479,0.0148,0.0,0.0
+8 V,0.0,0.0,0.99921,0.00038,0.0,0.0
+9 M,0.0,0.0,0.99955,3e-05,0.0,0.0
+10 M,0.0,0.0,0.99958,0.0,0.0,0.0
+11 I,0.0,0.0,0.99957,0.0,0.0,0.0
+12 A,0.0,0.0,0.99955,0.0,0.0,0.0
+13 C,0.0,0.0,0.99933,0.00021,0.0,0.0
+14 V,0.0,0.0,0.9995,2e-05,0.0,0.0
+15 V,0.0,0.0,0.99953,0.0,0.0,0.0
+16 V,0.0,0.0,0.99953,0.0,0.0,0.0
+17 F,0.0,0.0,0.99953,0.0,0.0,0.0
+18 I,0.0,0.0,0.99954,0.0,0.0,0.0
+19 A,0.0,0.0,0.99956,0.0,0.0,0.0
+20 M,0.0,0.0,0.99948,0.0,5e-05,0.0
+21 Q,0.0,0.0,0.99788,0.0,0.00164,0.0
+22 I,0.0,0.0,0.99017,0.0,0.00935,0.0
+23 L,0.0,0.0,0.86894,0.0,0.13061,0.0
+24 G,0.0,0.0,0.22113,0.0,0.7784,0.0
+25 D,0.0,0.0,0.00531,0.0,0.99422,0.0
+26 Q,0.0,0.0,4e-05,0.0,0.99948,0.0
+27 E,0.0,0.0,0.0,0.0,0.99954,0.0
+28 V,0.0,0.0,0.0,0.0,0.99954,0.0
+29 M,0.0,0.0,0.0,0.0,0.99957,0.0
+30 L,0.0,0.0,0.0,0.0,0.99957,0.0
+31 W,0.0,0.0,0.0,0.0,0.9996,0.0
+32 L,0.0,0.0,0.0,0.0,0.9996,0.0
+33 A,0.0,0.0,0.0,0.0,0.9996,0.0
+34 W,0.0,0.0,0.0,0.0,0.9996,0.0
+35 P,0.0,0.0,0.0,0.0,0.99963,0.0
+36 F,0.0,0.0,0.0,0.0,0.99963,0.0
+37 D,0.0,0.0,0.0,0.0,0.99966,0.0
+38 P,0.0,0.0,0.0,0.0,0.99966,0.0
+39 T,0.0,0.0,0.0,0.0,0.99969,0.0
+40 L,0.0,0.0,0.0,0.0,0.99969,0.0
+41 K,0.0,0.0,0.0,0.0,0.99969,0.0
+42 F,0.0,0.0,0.0,0.0,0.99969,0.0
+43 E,0.0,0.0,0.0,0.0,0.99969,0.0
+44 F,0.0,0.0,0.0,0.0,0.99973,0.0
+45 W,0.0,0.0,0.0,0.0,0.99976,0.0
+46 R,0.0,0.0,0.0,0.0,0.99976,0.0
+47 Y,0.0,0.0,3e-05,0.0,0.99973,0.0
+48 F,0.0,0.0,0.00047,0.0,0.99933,0.0
+49 T,0.0,0.0,0.00101,0.0,0.99878,0.0
+50 H,0.0,0.0,0.00757,0.0,0.99222,0.0
+51 A,0.0,0.0,0.82764,0.0,0.17215,0.0
+52 L,0.0,0.0,0.95624,0.0,0.04355,0.0
+53 M,0.0,0.0,0.99341,0.0,0.00638,0.0
+54 H,0.0,0.0,0.99423,0.0,0.00556,0.0
+55 F,0.0,0.0,0.99756,0.0,0.00223,0.0
+56 S,0.0,0.0,0.99919,0.0,0.00061,0.0
+57 L,0.0,0.0,0.99975,0.0,6e-05,0.0
+58 M,0.0,0.0,0.9998,0.0,1e-05,0.0
+59 H,0.0,0.0,0.99983,0.0,1e-05,0.0
+60 I,0.0,0.0,0.99982,0.0,0.0,0.0
+61 L,0.0,0.0,0.99983,0.0,0.0,0.0
+62 F,0.0,0.0,0.99984,0.0,0.0,0.0
+63 N,0.0,0.0,0.99985,0.0,0.0,0.0
+64 L,0.0,0.0,0.99985,0.0,0.0,0.0
+65 L,0.0,0.0,0.99985,0.0,0.0,0.0
+66 W,0.0,0.0,0.99985,0.0,0.0,0.0
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+68 W,0.0,0.0,0.99986,0.0,0.0,0.0
+69 Y,0.0,0.0,0.99975,0.00012,0.0,0.0
+70 L,0.0,0.0,0.99906,0.00081,0.0,0.0
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+99 Q,0.0,0.0,0.24375,0.0,0.75613,0.0
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+169 V,0.0,0.0,0.99987,4e-05,0.0,0.0
+170 G,0.0,0.0,0.9997,0.0002,0.0,0.0
+171 L,0.0,0.0,0.99991,0.0,0.0,0.0
+172 A,0.0,0.0,0.99991,0.0,0.0,0.0
+173 M,0.0,0.0,0.99992,0.0,0.0,0.0
+174 A,0.0,0.0,0.99992,0.0,0.0,0.0
+175 F,0.0,0.0,0.99984,9e-05,0.0,0.0
+176 V,0.0,0.0,0.99651,0.00345,0.0,0.0
+177 D,0.0,0.0,0.82865,0.1713,0.0,0.0
+178 S,0.0,0.0,0.68727,0.31267,0.0,0.0
+179 L,0.0,0.0,0.48774,0.5122,1e-05,0.0
+180 N,0.0,0.0,0.17987,0.82007,4e-05,0.0
+181 A,0.0,0.0,0.0,0.99973,0.00028,0.0

software/rosetta_ddG_pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/spanfiles/A/predicted_topologies.3line

@@ -0,0 +1,3 @@
+>input | TM
+ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA
+IIIIIMMMMMMMMMMMMMMMMMMMOOOOOOOOOOOOOOOOOOOOOOOOOOOMMMMMMMMMMMMMMMMMMMMMIIIIIIMMMMMMMMMMMMMMMMMMMMMOOMMMMMMMMMMMMMMMMMMMMMIIIIIIIIIIMMMMMMMMMMMMMMMMMMMMMMMOOOOMMMMMMMMMMMMMMMMMMMMMII

software/rosetta_ddG_pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/spanfiles/A/query.fasta

@@ -0,0 +1,2 @@
+> input
+ERAGPVTWVMMIACVVVFIAMQILGDQEVMLWLAWPFDPTLKFEFWRYFTHALMHFSLMHILFNLLWWWYLGGAVEKRLGSGKLIVITLISALLSGYVQQKFSGPWFGGLSGVVYALMGYVWLRGERDPQSGIYLQRGLIIFALIWIVAGWFDLFGMSMANGAHIAGLAVGLAMAFVDSLNA

software/rosetta_ddG_pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/spanfiles/input_A_A.span

@@ -0,0 +1,10 @@
+manual-generated spanfile from DeepTMHMM
+6 182
+antiparallel
+n2c
+		6	24
+		52	72
+		79	99
+		102	122
+		133	155
+		160	180

software/rosetta_ddG_pipeline/data/test/mp-pipeline/output/MPpipelineCreateGlpGTestCase_deepTMHMM/ddG/input/spanfiles/input_A_A_deepTMHMM.csv

@@ -0,0 +1,14 @@
+,ID,location,start,end,4,5,6,7
+0,input,inside,1,5,,,,
+1,input,TMhelix,6,24,,,,
+2,input,outside,25,51,,,,
+3,input,TMhelix,52,72,,,,
+4,input,inside,73,78,,,,
+5,input,TMhelix,79,99,,,,
+6,input,outside,100,101,,,,
+7,input,TMhelix,102,122,,,,
+8,input,inside,123,132,,,,
+9,input,TMhelix,133,155,,,,
+10,input,outside,156,159,,,,
+11,input,TMhelix,160,180,,,,
+12,input,inside,181,182,,,,