fix version incompatability

limit biopython to 1.73
fix overwriting of structures in backup temp file

rna_blast_analyze/BR_core/repredict_structures.py

@@ -133,7 +133,11 @@ def wrapped_ending_with_prediction(
     backup_file = args_inner.blast_in + '.tmp_rboAnalyzer'
     backup_base_obj = blastsearchrecompute2dict(analyzed_hits)
     with open(backup_file, 'w') as ff:
-        json.dump([backup_base_obj, {}, {}], ff, indent=2)
+        json.dump(
+            [backup_base_obj, {k: [seqrecord2dict(s) for s in v] for k, v in new_structures.items()}, exec_time],
+            ff,
+            indent=2
+        )
 
     # prediction methods present in analyzed_hits
     #  which might be loaded from intermediate file

setup.py

@@ -15,7 +15,7 @@
 }
 
 setup(
-    name='rna_blast_analyze',
+    name='rboAnalyzer',
     version=version,
     description='Analyze BLAST output for RNA query',
     author='Marek Schwarz',
@@ -28,10 +28,10 @@
     },
     install_requires=[
         'matplotlib',
-        'numpy',
+        'numpy>=1.14',
         'Jinja2>=2, <3',
         'pandas>=0.22',
-        'biopython>=1.72',
+        'biopython>=1.72, <1.74',
         'argcomplete',
     ],
     packages=['rna_blast_analyze', 'rna_blast_analyze.BR_core', 'rna_blast_analyze.BR_core.output'],

setup.py~

@@ -1,46 +1,40 @@
-from setuptools import setup, find_packages
+from setuptools import setup
 
-# package_data
-# - directly related to code
-# - 3rd_party_data as data_files not working to expectations
-
-with open('VERSION', 'r') as o:
+with open('rna_blast_analyze/VERSION', 'r') as o:
     version = o.read().strip()
 
 package_data = {
-    'rna_blast_analyze': [
+    'rboAnalyzer': [
         'BR_core/config.txt',
         'BR_core/prediction_parameters.json',
-        'BR_core/output/*.html',
-        'BR_core/output/style.css',
+        'BR_core/output/*',
         '3rd_party_source/RSEARCH_matrices/*',
-        'docs/*'
+        'docs/*',
+        'VERSION'
     ]
 }
 
 setup(
-    name='rna_blast_analyze',
+    name='rboAnalyzer',
     version=version,
     description='Analyze BLAST output for RNA query',
     author='Marek Schwarz',
     author_email='[email protected]',
     entry_points={
         'console_scripts': [
-            'rna_blast_analyze = rna_blast_analyze.BA:main',
+            'rboAnalyzer = rna_blast_analyze.BA:main',
             'genomes_from_blast = rna_blast_analyze.download_blast_genomes:main'
         ],
     },
     install_requires=[
         'matplotlib',
-        'dill',
-        'numpy',
+        'numpy>=1.14',
         'Jinja2>=2, <3',
         'pandas>=0.22',
-        'PyPDF2',
-        'biopython',
+        'biopython>=1.72, <1.74',
         'argcomplete',
     ],
-    packages=find_packages(),
+    packages=['rna_blast_analyze', 'rna_blast_analyze.BR_core', 'rna_blast_analyze.BR_core.output'],
     package_data=package_data,
     include_package_data=True,
 )

test_func/test_continue.py

@@ -2,11 +2,12 @@
 import os
 import tempfile
 import unittest
+from copy import copy
 
 from unittest.mock import patch
 
 from rna_blast_analyze.BR_core.BA_support import remove_files_with_try
-from rna_blast_analyze.BR_core.convert_classes import blastsearchrecomputefromdict, blastsearchrecompute2dict
+from rna_blast_analyze.BR_core.convert_classes import blastsearchrecomputefromdict, blastsearchrecompute2dict, seqrecord2dict
 from test_func.pseudoargs_class import Pseudoargs
 from test_func.test_execution import tab_output_equal, tab_output_equal_structures
 from rna_blast_analyze.BA import lunch_with_args
@@ -57,17 +58,18 @@ def setUp(self):
         os.close(ff)
         self.fasta_structures = fasta_structures
 
+    @patch('builtins.input', return_value='yes')
+    def test_continuation(self, mock_input):
+
         with open(blast_output, 'r') as f, open(backup_file, 'w') as ff:
             data = blastsearchrecomputefromdict(json.load(f))
-            data.args.json = None
             data.args.blast_in = blast_in
+            data.args.json = None
             for hit in data.hits:
                 del hit.extension.letter_annotations['rnafold']
 
             json.dump([blastsearchrecompute2dict(data), {}, {}], ff, indent=2)
 
-    @patch('builtins.input', return_value='yes')
-    def test_continuation(self, mock_input):
         out = lunch_with_args(self.args)
         self.assertEqual(1, 1)
 
@@ -105,3 +107,54 @@ def test_continuation(self, mock_input):
                 ],
                 'failed to delete: '
             )
+
+    @patch('builtins.input', return_value='yes')
+    def test_continuation2(self, mock_input):
+
+        with open(blast_output, 'r') as f, open(backup_file, 'w') as ff:
+            data = blastsearchrecomputefromdict(json.load(f))
+            data.args.blast_in = blast_in
+            data.args.json = None
+            data.args.prediction_method += ['centroid']
+
+            new_structures = {'rnafold': []}
+            for h in data.hits:
+                n = copy(h.extension)
+                n.letter_annotations['ss0'] = n.letter_annotations['rnafold']
+                del n.letter_annotations['rnafold']
+
+                new_structures['rnafold'].append(n)
+
+            json.dump([blastsearchrecompute2dict(data), {k: [seqrecord2dict(s) for s in v] for k, v in new_structures.items()}, {}], ff, indent=2)
+
+        out = lunch_with_args(self.args)
+        self.assertEqual(1, 1)
+
+        # test_output
+        for i in range(len(out)):
+            out[0].to_csv(self.csv)
+            j_obj = json.dumps(blastsearchrecompute2dict(out[0]), indent=2)
+            with open(self.json, 'w') as ff:
+                ff.write(j_obj)
+            out[0].write_results_fasta(self.fasta)
+            out[0].write_results_structures(self.fasta_structures)
+
+            t = tab_output_equal(
+                csvfile=self.csv,
+                jsonfile=self.json,
+                fastafile=self.fasta,
+                fastastructures=self.fasta_structures,
+                ref_seqs_file=os.path.join(fwd, test_data_dir, 'simple.json')
+            )
+            self.assertEqual(t, True)
+
+
+            remove_files_with_try(
+                [
+                    self.csv,
+                    self.json,
+                    self.fasta_structures,
+                    self.fasta,
+                ],
+                'failed to delete: '
+            )