fixed issue with long path for signalp

greedyFAS/annoFAS/annoFAS.py

@@ -237,6 +237,13 @@ def main():
     print('PID ' + str(os.getpid()))
     runAnnoFas([seqFile, outPath, toolPath, force, outName, eFlps, signalpOrg, eFeature, eInstance, hmmCores, redo,
                 extract, annoFile, cpus, annoToolFile])
+    # remove tmp folders
+    if os.path.exists('tmp/signalp'):
+        subfolders = [ f.path for f in os.scandir('tmp') if f.is_dir() ]
+        if len(subfolders) == 1 and subfolders[0] == "tmp/signalp":
+            shutil.rmtree('tmp')
+    if os.path.exists(f'{outPath}/tmp'):
+        shutil.rmtree(f'{outPath}/tmp')
     ende = time.time()
     print('Finished in ' + '{:5.3f}s'.format(ende-start))
 

greedyFAS/annoFAS/annoModules.py

@@ -191,17 +191,15 @@ def doSignalp(args):
     (seqFile, toolPath, org, outPath) = args
     # create tmp folder for signalp output
     seqFileName = seqFile.split('/')[-1].split('.')[0]
-    Path(outPath+'/tmp/signalp/'+seqFileName).mkdir(parents = True, exist_ok = True)
+    Path('/tmp/signalp/'+seqFileName).mkdir(parents = True, exist_ok = True)
     # load fasta seq
     inSeq = SeqIO.to_dict((SeqIO.parse(open(seqFile), 'fasta')))
-    # do signalp
-    cmd = '%s/SignalP/signalp -T %s/tmp/signalp/%s -t %s "%s"' % (toolPath, outPath, seqFileName, org, seqFile)
+    cmd = '%s/SignalP/signalp -T tmp/signalp/%s -t %s "%s"' % (toolPath, seqFileName, org, seqFile)
     try:
         signalpOut = subprocess.run([cmd], shell=True, capture_output=True, check=True)
     except:
         sys.exit('Error running\n%s' % cmd)
     lines = signalpOut.stdout.decode().split('\n')
-    # print(signalpOut.stdout.decode())
     # save to dict
     annoOut = {}
     if len(lines) > 0:
@@ -497,12 +495,14 @@ def doAnno(args):
         subprocess.run([rmCmd], shell=True, check=True)
     except:
         sys.exit('Error running\n%s' % rmCmd)
+    if len(os.listdir(f'{outPath}/tmp/{pid}')) == 0:
+        shutil.rmtree(f'{outPath}/tmp')
     if 'signalp' in toolList:
         try:
             seqFileName = seqFile.split('/')[-1].split('.')[0]
-            shutil.rmtree('%s/tmp/signalp/%s' % (outPath, seqFileName))
+            shutil.rmtree('tmp/signalp/%s' % seqFileName)
         except:
-            sys.exit('Error deleting %s/tmp/signalp/%s_%s' % (outPath, outNameTmp, seqIdTmp))
+            sys.exit('Error deleting tmp/signalp/%s_%s' % (outNameTmp, seqIdTmp))
     return final
 
 # functions for posprocessing annotation dictionary

greedyFAS/calcFAS.py

@@ -31,6 +31,7 @@
 from greedyFAS.mainFAS import fasInput, fasOutput, greedyFAS
 from greedyFAS.mainFAS.fasInput import read_json
 from pkg_resources import get_distribution
+import shutil
 
 
 def get_options():
@@ -344,7 +345,11 @@ def main():
         annojobs.append(args.ref_2)
     anno(annojobs, args, toolpath)
     fas((args, toolpath))
-
+    # remove tmp folders
+    if os.path.exists('tmp/signalp'):
+        subfolders = [ f.path for f in os.scandir('tmp') if f.is_dir() ]
+        if len(subfolders) == 1 and subfolders[0] == "tmp/signalp":
+            shutil.rmtree('tmp')
 
 if __name__ == '__main__':
     main()

setup.py

@@ -28,7 +28,7 @@
 
 setup(
     name='greedyFAS',
-    version='1.18.12',
+    version='1.18.13',
     python_requires='>=3.7.0',
     description='A tool to compare protein feature architectures',
     long_description=long_description,