Version up, update viennarna

barricklab · Aug 5, 2024 · 0a99c04 · 0a99c04
1 parent d9a779f
commit 0a99c04
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Showing 10 changed files with 384 additions and 373 deletions.
diff --git a/environment.yml b/environment.yml
@@ -5,7 +5,7 @@ channels:
   - defaults
 dependencies:
   - python>=3.8.1
-  - viennarna==2.4.18
+  - viennarna==2.6.4
   - setuptools
   - wheel
   - numpy
diff --git a/ostir/ViennaRNA.py b/ostir/ViennaRNA.py
@@ -15,7 +15,7 @@
 import sys
 import re
 import RNA
-
+import time
 
 #  On import check dependencies
 dependencies = [which('RNAfold') is not None,
@@ -98,7 +98,15 @@ def subopt(sequences, constraints, energy_gap, temp = 37.0, dangles = "some"):
             constraints = constraints + "."*len(sequences[1])
         rna.hc_add_from_db(constraints)
 
-    vienna_subopt = rna.subopt(int((energy_gap+2.481)*100))
+    # Get ahead of VRNA adjustment to suppress warning
+    _, _, mfe_energy = mfe(sequences, constraints, temp, dangles)
+    threshold = int((energy_gap+2.481)*100)
+    if threshold+mfe_energy*100 > 10_000_000:
+        threshold = -1
+
+    vienna_subopt = rna.subopt(threshold)
+
+    time.sleep(1)
     subopt_output = [[str(output.structure), str(round(output.energy, 3))] for output in vienna_subopt]
 
     subopt_energy = []
@@ -111,7 +119,7 @@ def subopt(sequences, constraints, energy_gap, temp = 37.0, dangles = "some"):
         subopt_output = process_fold_outputs(subopt_output, multi_sequence=False)
 
     for finding in subopt_output:
-        
+
         subopt_energy.append(float(finding[1]))
         subopt_basepairing_x.append(finding[2])
         subopt_basepairing_y.append(finding[3])
@@ -120,7 +128,7 @@ def subopt(sequences, constraints, energy_gap, temp = 37.0, dangles = "some"):
     return subopt_energy, subopt_basepairing_x, subopt_basepairing_y
 
 
-def energy(sequences, base_pairing_x, base_pairing_y, Temp, dangles): 
+def energy(sequences, base_pairing_x, base_pairing_y, Temp, dangles):
     if Temp <= 0: raise ValueError("The specified temperature must be greater than zero.")
     temp = Temp
 

diff --git a/ostir/ostir.py b/ostir/ostir.py
@@ -31,7 +31,7 @@
     rprint = None
 
 OSTIR_VERSION = '1.1.1'
-OLDEST_VIENNA = '2.4.18'
+OLDEST_VIENNA = '2.6.4'
 
 # The E. coli sequence
 Ecoli_anti_Shine_Dalgarno = 'ACCTCCTTA'
@@ -246,7 +246,7 @@ def _print_output(outdict):
                                 str(start['dG_start_codon']))
 
             console.print(table)
-            
+
 def save_to_csv(column_names, outdict, outfile):
     with open(outfile, 'w', encoding='utf8') as output_file:
         dict_writer = csv.DictWriter(output_file, column_names, lineterminator="\n")
@@ -298,7 +298,7 @@ def main():
         dest='v',
         required=False,
         default="1",
-        help="Sets the verbosity level. Default 0 is quiet, 1 is normal, 2 is verbose",
+        help="Sets the verbosity level. 0 is quiet, default 1 is normal, 2 is verbose",
     )
 
     parser.add_argument(
@@ -439,6 +439,8 @@ def main():
             sys.exit(1)
         cmd_kwargs['verbosity'] = int(options.v)
         verbosity = cmd_kwargs['verbosity']
+    else:
+        verbosity = 1
 
     # Check if viennaRNA is installed
     dependencies = [which('RNAfold') is not None,
@@ -632,7 +634,7 @@ def main():
                     value_dict['anti-Shine-Dalgarno'] = run_metadata[key].get('anti-Shine-Dalgarno') or run_metadata[key].get('asd') or cmd_kwargs.get('aSD')
                 result_set.append(value_dict)
             results.extend(result_set)
-        
+
 
     ## Output - for all ways of running ##############################################################
     if outfile:

diff --git a/setup.py b/setup.py
@@ -6,7 +6,7 @@
 
 setuptools.setup(
     name="OSTIR",
-    version="1.1.2",
+    version="1.1.3",
     author="Cameron Roots, Alexandra Lukasiewicz, Jeffrey Barrick, ",
     author_email="[email protected]",
     description="Open Source Transcription Initiation Rates",

diff --git a/tests/expected/Salis2009.csv b/tests/expected/Salis2009.csv
diff --git a/tests/expected/T7_genome.csv b/tests/expected/T7_genome.csv
diff --git a/tests/expected/command_line_CSV_input.csv b/tests/expected/command_line_CSV_input.csv
@@ -1,4 +1,4 @@
-name,start_codon,start_position,expression,RBS_distance_bp,dG_total,dG_rRNA:mRNA,dG_mRNA,dG_spacing,dG_standby,dG_start_codon
-sequence_1,ATG,38,643.9384,4,2.0289,-8.381,-11.6,0.0039,0.0,-1.194
-sequence_1,ATG,71,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
-sequence_1,ATG,89,227.5882,4,4.6289,-0.681,-6.5,0.0039,0.0,-1.194
+name,start_codon,start_position,expression,RBS_distance_bp,dG_total,dG_rRNA:mRNA,dG_mRNA,dG_spacing,dG_standby,dG_start_codon
+sequence_1,ATG,38,643.9384,4,2.0289,-8.381,-11.6,0.0039,0.0,-1.194
+sequence_1,ATG,71,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
+sequence_1,ATG,89,227.5882,4,4.6289,-0.681,-6.5,0.0039,0.0,-1.194
diff --git a/tests/expected/command_line_CSV_input_alternate_columns_and_defaults.csv b/tests/expected/command_line_CSV_input_alternate_columns_and_defaults.csv
@@ -1,9 +1,9 @@
-name,anti-Shine-Dalgarno,sequence,start_codon,start_position,expression,RBS_distance_bp,dG_total,dG_rRNA:mRNA,dG_mRNA,dG_spacing,dG_standby,dG_start_codon
-first_sequence,ACCTCCTTA,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,38,643.9384,4,2.0289,-8.381,-11.6,0.0039,0.0,-1.194
-first_sequence,ACCTCCTTA,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,71,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
-first_sequence,ACCTCCTTA,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,89,227.5882,4,4.6289,-0.681,-6.5,0.0039,0.0,-1.194
-second_sequence,TCTGAAGAC,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,38,34.6638,7,9.3332,-1.881,-11.6,0.8082,0.0,-1.194
-second_sequence,TCTGAAGAC,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,71,40.1662,6,8.9649,-3.981,-13.8,0.3399,0.0,-1.194
-second_sequence,TCTGAAGAC,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,89,460.8985,6,2.8649,-3.381,-6.5,0.3399,-0.6,-1.194
-sequence_3,CCCCCCCCC,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,38,44.2111,5,8.725,-1.681,-11.6,0.0,0.0,-1.194
-sequence_3,CCCCCCCCC,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,71,0.0017,22,34.1706,-1.681,-13.8,23.2456,0.0,-1.194
+name,anti-Shine-Dalgarno,sequence,start_codon,start_position,expression,RBS_distance_bp,dG_total,dG_rRNA:mRNA,dG_mRNA,dG_spacing,dG_standby,dG_start_codon
+first_sequence,ACCTCCTTA,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,38,643.9384,4,2.0289,-8.381,-11.6,0.0039,0.0,-1.194
+first_sequence,ACCTCCTTA,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,71,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
+first_sequence,ACCTCCTTA,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,89,227.5882,4,4.6289,-0.681,-6.5,0.0039,0.0,-1.194
+second_sequence,TCTGAAGAC,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,38,34.6638,7,9.3332,-1.881,-11.6,0.8082,0.0,-1.194
+second_sequence,TCTGAAGAC,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,71,40.1662,6,8.9649,-3.981,-13.8,0.3399,0.0,-1.194
+second_sequence,TCTGAAGAC,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,89,460.8985,6,2.8649,-3.381,-6.5,0.3399,-0.6,-1.194
+sequence_3,CCCCCCCCC,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,38,44.2111,5,8.725,-1.681,-11.6,0.0,0.0,-1.194
+sequence_3,CCCCCCCCC,TTCTAGActttaatttaacgtaaataaggaagtcattATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATGGA,ATG,71,0.0017,22,34.1706,-1.681,-13.8,23.2456,0.0,-1.194
diff --git a/tests/expected/command_line_FASTA_input.csv b/tests/expected/command_line_FASTA_input.csv
@@ -1,15 +1,15 @@
-name,start_codon,start_position,expression,RBS_distance_bp,dG_total,dG_rRNA:mRNA,dG_mRNA,dG_spacing,dG_standby,dG_start_codon
-Seq1-1,ATG,24,53.8087,0,8.2339,-15.981,-8.2,17.2089,0.0,-1.194
-Seq1-1,ATG,57,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
-Seq1-1,ATG,75,227.5882,4,4.6289,-0.681,-6.5,0.0039,0.0,-1.194
-Seq1-2,ATG,25,54.3225,1,8.2101,-15.981,-8.2,17.1851,0.0,-1.194
-Seq1-2,ATG,58,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
-Seq1-2,ATG,76,227.5882,4,4.6289,-0.681,-6.5,0.0039,0.0,-1.194
-Seq1-3,ATG,26,72.9191,2,7.4741,-15.981,-8.2,16.4491,0.0,-1.194
-Seq1-3,ATG,59,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
-Seq1-3,ATG,77,382.8221,4,3.3289,-0.681,-5.2,0.0039,0.0,-1.194
-Seq1-4,ATG,27,6409.905,3,-3.7158,-15.981,-8.2,5.2592,0.0,-1.194
-Seq1-4,ATG,60,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
-Seq1-4,ATG,78,571.1179,4,2.3289,-0.681,-4.2,0.0039,0.0,-1.194
-Seq1-5,ATG,28,52463.8398,4,-8.9711,-15.981,-8.2,0.0039,0.0,-1.194
-Seq1-5,ATG,61,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
+name,start_codon,start_position,expression,RBS_distance_bp,dG_total,dG_rRNA:mRNA,dG_mRNA,dG_spacing,dG_standby,dG_start_codon
+Seq1-1,ATG,24,53.8087,0,8.2339,-15.981,-8.2,17.2089,0.0,-1.194
+Seq1-1,ATG,57,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
+Seq1-1,ATG,75,227.5882,4,4.6289,-0.681,-6.5,0.0039,0.0,-1.194
+Seq1-2,ATG,25,54.3225,1,8.2101,-15.981,-8.2,17.1851,0.0,-1.194
+Seq1-2,ATG,58,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
+Seq1-2,ATG,76,227.5882,4,4.6289,-0.681,-6.5,0.0039,0.0,-1.194
+Seq1-3,ATG,26,72.9191,2,7.4741,-15.981,-8.2,16.4491,0.0,-1.194
+Seq1-3,ATG,59,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
+Seq1-3,ATG,77,382.8221,4,3.3289,-0.681,-5.2,0.0039,0.0,-1.194
+Seq1-4,ATG,27,6409.905,3,-3.7158,-15.981,-8.2,5.2592,0.0,-1.194
+Seq1-4,ATG,60,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
+Seq1-4,ATG,78,571.1179,4,2.3289,-0.681,-4.2,0.0039,0.0,-1.194
+Seq1-5,ATG,28,52463.8398,4,-8.9711,-15.981,-8.2,0.0039,0.0,-1.194
+Seq1-5,ATG,61,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
diff --git a/tests/expected/command_line_string_input.csv b/tests/expected/command_line_string_input.csv
@@ -1,4 +1,4 @@
-name,sequence,start_codon,start_position,expression,RBS_distance_bp,dG_total,dG_rRNA:mRNA,dG_mRNA,dG_spacing,dG_standby,dG_start_codon
-unnamed,TTCTAGAAAAAAAATAAGGAGGTAAAATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATG,ATG,27,6409.905,3,-3.7158,-15.981,-8.2,5.2592,0.0,-1.194
-unnamed,TTCTAGAAAAAAAATAAGGAGGTAAAATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATG,ATG,60,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
-unnamed,TTCTAGAAAAAAAATAAGGAGGTAAAATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATG,ATG,78,571.1179,4,2.3289,-0.681,-4.2,0.0039,0.0,-1.194
+name,sequence,start_codon,start_position,expression,RBS_distance_bp,dG_total,dG_rRNA:mRNA,dG_mRNA,dG_spacing,dG_standby,dG_start_codon
+unnamed,TTCTAGAAAAAAAATAAGGAGGTAAAATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATG,ATG,27,6409.905,3,-3.7158,-15.981,-8.2,5.2592,0.0,-1.194
+unnamed,TTCTAGAAAAAAAATAAGGAGGTAAAATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATG,ATG,60,0.0558,1,25.4101,-4.381,-13.8,17.1851,0.0,-1.194
+unnamed,TTCTAGAAAAAAAATAAGGAGGTAAAATGGCGAGCTCTGAAGACGTTATCAAAGAGTTCATGCGTTTCAAAGTTCGTATG,ATG,78,571.1179,4,2.3289,-0.681,-4.2,0.0039,0.0,-1.194