minor fixes, locarna max version set

set max major version in readme.

readme.md

@@ -60,28 +60,28 @@ conda install -c conda-forge -c bioconda -c schwarz.marek rboanalyzer
 ### Install from source
 
  __Prerequisites__
-- python >= 3.4 [link](https://www.python.org/downloads/)   
+- python >= 3.4, <3.8 [link](https://www.python.org/downloads/)
   Verify that you have working up-to date `pip3`.
   ```
   pip3 install --upgrade pip
   # or
   pip3 install --upgrade pip --user
   ```
 - ncbi-blast+ >= 2.6, < 2.8.1 [link](http://ftp.ncbi.nih.gov/blast/executables/blast+/2.7.1/)
-- locarna >= 1.9.2 [link](https://github.com/s-will/LocARNA/releases/tag/v1.9.2.2)
-- infernal >= 1.1 [link](http://eddylab.org/infernal/)
-- clustalo >= 1.2.4 [link](http://www.clustal.org/omega/)
-- muscle >= 3.8.31 [link](https://www.drive5.com/muscle/downloads.htm)
+- locarna >= 1.9.2, <2 [link](https://github.com/s-will/LocARNA/releases/tag/v1.9.2.2)
+- infernal >= 1.1, <2 [link](http://eddylab.org/infernal/)
+- clustalo >= 1.2.4, <2 [link](http://www.clustal.org/omega/)
+- muscle >= 3.8.31, <4 [link](https://www.drive5.com/muscle/downloads.htm)
 
 For prediction:
-- viennarna >=2.3.5 (with refold.pl in PATH) [link](https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_3_x/ViennaRNA-2.3.5.tar.gz)   
+- viennarna >=2.3.5, <3 (with refold.pl in PATH) [link](https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_3_x/ViennaRNA-2.3.5.tar.gz)
   Don't forget to add `refold.pl` to your `PATH`. The `refold.pl` script is located in the `ViennaRNA-[version]/src/Utils/`.
 - centroid_homfold >= 0.0.15 [link](https://github.com/satoken/centroid-rna-package/releases/tag/v0.0.15)
-- RNAstructure >= 6.0 (TurboFold - Text (Command Line) Interfaces ) [link](https://rna.urmc.rochester.edu/RNAstructure.html)   
+- RNAstructure >= 6.0, <7 (TurboFold - Text (Command Line) Interfaces ) [link](https://rna.urmc.rochester.edu/RNAstructure.html)
   Don't forget to set the `DATAPATH` environment variable [link](http://rna.urmc.rochester.edu/Text/Thermodynamics.html).
 
 Optional (some prediction methods are not available without):
-- UNAFold >= 3.8 [link](http://unafold.rna.albany.edu/?q=DINAMelt/software)
+- UNAFold >= 3.8, <4 [link](http://unafold.rna.albany.edu/?q=DINAMelt/software)
 
 Clone or download this repository, unpack it if needed. Go to directory with the source code for the rboAnalyzer and run
 

rna_blast_analyze/BA.py

@@ -531,6 +531,8 @@ def lunch_with_args(args):
     # ========= run =========
     blast_fn = os.path.basename(args.blast_in) + '.r-' + hashstring[:10]
     blast_dir = os.path.dirname(args.blast_in)
+    if blast_dir == '':
+        blast_dir = os.getcwd()
     potential_matches = [f for f in os.listdir(blast_dir) if f == blast_fn]
     if len(potential_matches) == 0:
         with open(args.blast_in + '.r-' + args.sha1[:10], 'w') as f:

rna_blast_analyze/BR_core/BA_support.py

@@ -255,7 +255,7 @@ def run_muscle(fasta_file, out_file=None, muscle_params='', reorder=True):
         ]
     ml.debug(cmd)
 
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         r = call(cmd, stdout=tmp, stderr=tmp)
         if r:
             msgfail = 'Call to muscle failed.'
@@ -286,7 +286,7 @@ def run_muscle(fasta_file, out_file=None, muscle_params='', reorder=True):
 
 def RNAfold(sequence):
     ml.debug(fname())
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         r = check_output(
             [
                 '{}RNAfold'.format(CONFIG.viennarna_path),

rna_blast_analyze/BR_core/BA_verify.py

@@ -10,7 +10,7 @@
 from rna_blast_analyze.BR_core.tools_versions import blast_minimal_version, locarna_minimal_version, \
     infernal_minimal_version, vrna_minimal_version, clustalo_minimal_version, muscle_minimal_version, \
     centroid_homfold_minimal_version, turbofold_minimal_version,\
-    mfold_minimal_version, method_required_tools, blast_maximal_version
+    mfold_minimal_version, method_required_tools, blast_maximal_version, locarna_maximal_version
 
 ml = logging.getLogger('rboAnalyzer')
 
@@ -47,7 +47,7 @@ def verify_blastdbcmd(minimal_version, maximal_version):
         return False
 
 
-def verify_locarna(minimal_version):
+def verify_locarna(minimal_version, maximal_version):
     msgversion = 'Locarna is not installed in required version, required version is {}.{}.{}'.format(*locarna_minimal_version)
     msgpath = '{}LocARNA could not be located (not in PATH).'.format(CONFIG.locarna_path)
     msgsuccess = 'Locarna is installed in required version'
@@ -61,7 +61,12 @@ def verify_locarna(minimal_version):
         a = a.decode()
         if a.startswith('LocARNA'):
             r = [int(m.group()) for m in re.finditer('[0-9]+', a)]
-            return version_check(r, minimal_version, msgsuccess, msgversion)
+            bb_min = version_check(r, minimal_version, msgsuccess, msgversion)
+            bb_max = version_check(r, maximal_version, msgsuccess, msgversion, operator.le)
+            if bb_min and bb_max:
+                return True
+            else:
+                return False
         else:
             ml.warning(msgversion)
             return False
@@ -313,7 +318,7 @@ def check_3rd_party_tools():
     if verify_blastdbcmd(blast_minimal_version, blast_maximal_version):
         installed.add('blastdbcmd')
 
-    if verify_locarna(locarna_minimal_version):
+    if verify_locarna(locarna_minimal_version, locarna_maximal_version):
         installed.add('locarna')
 
     if verify_infernal('cmbuild', infernal_minimal_version):

rna_blast_analyze/BR_core/alifold4all.py

@@ -18,7 +18,7 @@ def compute_clustalo_clasic(file, clustalo_params=''):
     fd, out_path = mkstemp(prefix='rba_', suffix='_01', dir=CONFIG.tmpdir)
     os.close(fd)
 
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         parlist = clustalo_params.split()
         cmd = [
             '{}clustalo'.format(CONFIG.clustal_path),
@@ -45,7 +45,7 @@ def compute_alifold(msa_file, alifold_params=''):
     fd, out_path = mkstemp(prefix='rba_', suffix='_02', dir=CONFIG.tmpdir)
     os.close(fd)
 
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         cmd = '{} --noPS -f C {} < {} > {}'.format(
             shlex.quote('{}RNAalifold'.format(CONFIG.viennarna_path)),
             ' '.join([shlex.quote(i) for i in shlex.split(alifold_params)]),
@@ -81,7 +81,7 @@ def compute_refold(alig_file, cons_file):
         shlex.quote(out_path)
     )
     ml.debug(cmd)
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         r = call(cmd, shell=True, stdout=tmp, stderr=tmp)
         if r:
             msgfail = 'Call to refold.pl failed.'

rna_blast_analyze/BR_core/centroid_homfold.py

@@ -33,7 +33,7 @@ def run_centroid_homfold(fasta2predict, fasta_homologous_seqs, centroid_homfold_
         '-o', ch_outfile,
         fasta2predict
     ]
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         r = call(cmd, stdout=tmp, stderr=tmp)
         if r:
             tmp.seek(0)

rna_blast_analyze/BR_core/cmalign.py

@@ -44,7 +44,7 @@ def run_cmscan(fastafile, cmmodels_file=None, params=None, outfile=None, threads
     else:
         cm_file = os.path.join(rfam.rfam_dir, rfam.rfam_file_name)
 
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
 
         # build commandline
         cmd = ['{}cmscan'.format(CONFIG.infernal_path)]
@@ -83,7 +83,7 @@ def run_cmfetch(cmfile, modelid, outfile=None):
         fd, out = mkstemp(prefix='rba_', suffix='_11', dir=CONFIG.tmpdir)
         os.close(fd)
 
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         cmd = [
             '{}cmfetch'.format(CONFIG.infernal_path),
             '-o', out,
@@ -116,7 +116,7 @@ def run_cmemit(model, params='', out_file=None):
         fd, out = mkstemp(prefix='rba_', suffix='_12', dir=CONFIG.tmpdir)
         os.close(fd)
 
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         # build commandline
         cmd = ['{}cmemit'.format(CONFIG.infernal_path)]
         if params != '':
@@ -266,40 +266,46 @@ def download_cmmodels_file(path=None, url=None):
     ml.debug(cmd)
 
     ml.info('Downloading RFAM database (aprox 300Mb). This may take a while...')
-    with TemporaryFile(mode='w+') as tmp:
-        r = check_output(cmd, stderr=tmp)
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
+        r = call(cmd, stderr=tmp, stdout=tmp)
 
-        if not r:
+        if r:
             msgfail = 'Call to wget failed. Please check the internet connection and/or availability of "wget".'
             ml.error(msgfail)
             ml.debug(cmd)
             sys.exit(1)
 
-    if 'Remote file no newer than local file ‘Rfam.cm.gz’ -- not retrieving.' in r.decode():
-        # do not download
-        ml.info('No new data. Nothing to do.')
-    else:
-        # unzip using build in gzip
-        with gzip.open(os.path.join(path, rfam.gzname), 'rb') as fin:
-            with open(os.path.join(path, rfam.rfam_file_name), 'wb') as fout:
-                shutil.copyfileobj(fin, fout)
-
-        # run cmpress to create binary files needed to run cmscan
-        try:
-            run_cmpress(os.path.join(path, rfam.rfam_file_name))
-        except exceptions.CmpressException as e:
-            ml.error(str(e))
-            ml.error('The Rfam file might be corrupt. Please check following output to get more information.\n')
-            print(e.errors)
-            sys.exit(1)
+        tmp.seek(0)
+        cmd_output = tmp.read()
+
+        if 'Remote file no newer than local file' in cmd_output:
+            # do not download
+            msg = 'No new data. Nothing to do.'
+            ml.info(msg)
+            if ml.getEffectiveLevel() > 20:
+                print(msg)
+        else:
+            # unzip using build in gzip
+            with gzip.open(os.path.join(path, rfam.gzname), 'rb') as fin:
+                with open(os.path.join(path, rfam.rfam_file_name), 'wb') as fout:
+                    shutil.copyfileobj(fin, fout)
+
+            # run cmpress to create binary files needed to run cmscan
+            try:
+                run_cmpress(os.path.join(path, rfam.rfam_file_name))
+            except exceptions.CmpressException as e:
+                ml.error(str(e))
+                ml.error('The Rfam file might be corrupt. Please check following output to get more information.\n')
+                print(e.errors)
+                sys.exit(1)
 
-    return os.path.join(path, rfam.rfam_file_name)
+        return os.path.join(path, rfam.rfam_file_name)
 
 
 def run_cmpress(file2process):
     ml.info('Running cmpress.')
     ml.debug(fname())
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         cmd = ['{}cmpress'.format(CONFIG.infernal_path), '-F', file2process]
         ml.debug(cmd)
         r = call(cmd, stdout=tmp, stderr=tmp)
@@ -328,7 +334,7 @@ def run_cmbuild(cmbuild_input_file, cmbuild_params=''):
     cm_fd, cm_file = mkstemp(prefix='rba_', suffix='_13', dir=CONFIG.tmpdir)
     os.close(cm_fd)
 
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         cmd = ['{}cmbuild'.format(CONFIG.infernal_path), '-F']
         if cmbuild_params != '':
             cmd += cmbuild_params.split()
@@ -358,7 +364,7 @@ def run_cmalign_on_fasta(fasta_file, model_file, cmalign_params='--notrunc', ali
     cma_fd, cma_file = mkstemp(prefix='rba_', suffix='_14', dir=CONFIG.tmpdir)
     os.close(cma_fd)
 
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         cmd = [
             '{}cmalign'.format(CONFIG.infernal_path),
             '--informat', 'fasta',

rna_blast_analyze/BR_core/expand_by_LOCARNA.py

@@ -299,7 +299,7 @@ def run_locarna(query_file, subject_file, locarna_params):
         shlex.quote(subject_file + '.loc_out'),
     )
     ml.debug(cmd)
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         r = call(cmd, shell=True, stdout=tmp, stderr=tmp)
         if r:
             msgfail = 'Call to locarna failed for files in1:{} in2:{} out:{}'.format(

rna_blast_analyze/BR_core/hybrid_ss_min.py

@@ -30,7 +30,7 @@ def _run_hybrid_ss_min_wrapper(seq, P, W, M):
 
 
 def _run_hybrid_ss_min_single(file_path, P, W, M):
-    with TemporaryFile(mode='w') as tmp:
+    with TemporaryFile(mode='w', encoding='utf-8') as tmp:
         cmd3 = [
             '{}hybrid-ss-min'.format(CONFIG.mfold_path),
             '--suffix=DAT',

rna_blast_analyze/BR_core/predict_structures.py

@@ -837,7 +837,7 @@ def _try_rescue(profile_file):
         c_fd, clustalo_file = mkstemp(prefix='rba_', suffix='_57', dir=CONFIG.tmpdir)
         os.close(c_fd)
 
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         cmd = [
             '{}clustalo'.format(CONFIG.clustal_path),
             '--force',

rna_blast_analyze/BR_core/tools_versions.py

@@ -1,6 +1,7 @@
 blast_minimal_version = [2, 6, 0]
 blast_maximal_version = [2, 8, 0]
 locarna_minimal_version = [1, 9, 2]
+locarna_maximal_version = [1, 999, 999]
 infernal_minimal_version = [1, 1, 2]
 vrna_minimal_version = [2, 3, 5]
 clustalo_minimal_version = [1, 2, 4]

rna_blast_analyze/BR_core/turbofold.py

@@ -193,7 +193,7 @@ def _turbofold_worker(sequences, params):
     )
 
     # run without prediction progress reporting output
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         cmd = [
             '{}TurboFold'.format(CONFIG.turbofold_path),
             con_file

rna_blast_analyze/BR_core/viennaRNA.py

@@ -27,7 +27,7 @@ def rnafold(fastafile, outfile, parameters=''):
         shlex.quote(outfile)
     )
     ml.debug(cmd)
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         r = call(cmd, shell=True, stderr=tmp, stdout=tmp)
 
         if r:
@@ -80,7 +80,7 @@ def run_rnaplot(seq, structure=None, format='svg', outfile=None):
         shlex.quote(tmpfile)
     )
     ml.debug(cmd)
-    with TemporaryFile(mode='w+') as tmp:
+    with TemporaryFile(mode='w+', encoding='utf-8') as tmp:
         r = call(cmd, shell=True, stdout=tmp, stderr=tmp)
         if r:
             msgfail = 'Call to RNAplot failed.'