Catch exception when there are no short variations between the genomes.

schneebergerlab · Dec 11, 2024 · 30d4511 · 30d4511
1 parent df86063
commit 30d4511
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Showing 3 changed files with 12 additions and 5 deletions.
diff --git a/syri/__init__.py b/syri/__init__.py
@@ -1 +1 @@
-__version__ = "1.7.0"
+__version__ = "1.7.1"
diff --git a/syri/pyxFiles/findshv.pyx b/syri/pyxFiles/findshv.pyx
@@ -190,8 +190,16 @@ def getshv(args, coords, chrlink):
             logger.error('Error in finding SNPs using show-snps: ' + out[1].decode())
             sys.exit()
         else:
-            allsnps = pd.read_table(cwdpath + prefix + fname, header = None)
-            logger.debug('finished writing SNPs')
+            try:
+                allsnps = pd.read_table(cwdpath + prefix + fname, header = None)
+                logger.debug('finished writing SNPs')
+            except pd.errors.EmptyDataError as e:
+                logger.warning('No SNPs or small indels were identified in the alignments.')
+                if mapit == 1:
+                    fileRemove(cwdpath + prefix + fname)
+                with open(cwdpath + prefix + 'snps.txt', "w") as fout:
+                    pass
+                return None
 
         achrs = pd.unique(allAlignments['aChr'])
         bchrs = pd.unique(allAlignments['bChr'])

diff --git a/syri/pyxFiles/findsv.pyx b/syri/pyxFiles/findsv.pyx
@@ -109,8 +109,7 @@ def getSV(cwdPath, allAlignments, prefix, offset):
     logger = logging.getLogger("getSV")
     offset = -abs(offset)
     fout = open(cwdPath + prefix + "sv.txt", "w")
-    allAlignments["id"] = allAlignments.group.astype(
-        "str") + 'Chr' + allAlignments.aChr + 'Chr' + allAlignments.bChr + allAlignments.state
+    allAlignments["id"] = allAlignments.group.astype("str") + 'Chr' + allAlignments.aChr + 'Chr' + allAlignments.bChr + allAlignments.state
     allBlocks = pd.unique(allAlignments.id)
 
     for i in allBlocks: