Protect against same input/output file for trim.py

davidemms · Jul 8, 2021 · 1b3f37c · 1b3f37c
1 parent cf3bcc9
commit 1b3f37c
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Showing 3 changed files with 5 additions and 4 deletions.
diff --git a/scripts_of/trim.py b/scripts_of/trim.py
@@ -85,8 +85,9 @@ def main(infn, outfn, f=0.1, n_min=500, c=0.75):
         print("ERROR, input file does not exist: %s" % infn)
         sys.exit()
     try:
-        with open(outfn, 'w') as outfile:
-            outfile.write("\n")
+        # BEWARE: Input and output files may be the same
+        with open(outfn, 'a') as outfile:
+            outfile.write(" ")
     except:
         print("ERROR, cannot write to output file: %s" % outfn)
         sys.exit()

diff --git a/scripts_of/util.py b/scripts_of/util.py
@@ -49,7 +49,7 @@
 SequencesInfo = namedtuple("SequencesInfo", "nSeqs nSpecies speciesToUse seqStartingIndices nSeqsPerSpecies")    # speciesToUse - list of ints
 
 picProtocol = 1
-version = "2.5.3"
+version = "2.5.4"
 
 def PrintNoNewLine(text):
     parallel_task_manager.PrintNoNewLine(text)

diff --git a/tests/test_orthofinder.py b/tests/test_orthofinder.py
@@ -42,7 +42,7 @@
 goldResultsDir_smallExample = baseDir + "ExpectedOutput/SmallExampleDataset/"
 goldPrepareBlastDir = baseDir + "ExpectedOutput/SmallExampleDataset_PreparedForBlast/"
 
-version = "2.5.2"
+version = "2.5.4"
 requiredBlastVersion = "2.2.28+"
 
 standard_new_files = ("Orthogroups.csv Orthogroups.GeneCount.csv SingleCopyOrthogroups.txt Orthogroups_UnassignedGenes.csv Orthogroups.txt clusters_OrthoFinder_I1.5.txt_id_pairs.txt clusters_OrthoFinder_I1.5.txt OrthoFinder_graph.txt Statistics_PerSpecies.csv Statistics_Overall.csv Orthogroups_SpeciesOverlaps.csv").split()