added proper spatype.txt corruption errormessage

scripts/spaTypesToSequences.py

-from Bio import SeqIO
 import re
 
+from Bio import SeqIO
+
 regSpaTypes = re.compile(r'((t[0-9]+,)([0-9][0-9])+(-[0-9])*)')
-#Load repeat sequences in fasta format
-repeats = SeqIO.parse(snakemake.input['repeats'],'fasta')
+# Load repeat sequences in fasta format
+repeats = SeqIO.parse(snakemake.input['repeats'], 'fasta')
 
 repeatsDict = {}
 
 filterList = []
 
-#Pre-Process Repeats
+# Pre-Process Repeats
 
 if 'filterList' in snakemake.input:
-	with open(snakemake.input['filterList'],'r') as infile:
-		filterList = infile.read().split(',')
+    with open(snakemake.input['filterList'], 'r') as infile:
+        filterList = infile.read().split(',')
 
 for repeat in repeats:
-	repeatsDict[repeat.id[1:]]=str(repeat.seq)
-
-with open(snakemake.input['types'],'r') as infile, open(snakemake.output['out'],'w') as outfile:
-	spaTypes = infile.read().splitlines()
-	spaTypesExtended = []
-	
-	for line, spaType in enumerate(spaTypes):
-		if not regSpaTypes.match(spaType):
-			print("spaType in spatypes" + " does not fit into the pattern: " + spaType + "in line " + str(line+1))
-		split = spaType.split(',')
-		name = split[0]
-		if len(filterList) > 0:
-			if not name in filterList:
-				continue
-		value = split[1]
-		sptRepeats = value.split('-')
-		if not sptRepeats:
-			continue
-		sequence = ''
-		for repeat in sptRepeats:
-			if repeat not in repeatsDict:
-				print("Unrecoginized repeat in spatype " + repeat + ", found in line " + str(line+1))
-			sequence += repeatsDict[repeat]
-		outfile.write('>'+name+'\n'+sequence+'\n')
+    repeatsDict[repeat.id[1:]] = str(repeat.seq)
+
+with open(snakemake.input['types'], 'r') as infile, open(snakemake.output['out'], 'w') as outfile:
+    spaTypes = infile.read().splitlines()
+    spaTypesExtended = []
+
+    for line, spaType in enumerate(spaTypes):
+        if not regSpaTypes.match(spaType):
+            print("spaType in spatypes" + " does not fit into the pattern: " + spaType + "in line " + str(line + 1))
+        split = spaType.split(',')
+        name = split[0]
+        if len(filterList) > 0:
+            if not name in filterList:
+                continue
+        value = split[1]
+        sptRepeats = value.split('-')
+        if not sptRepeats:
+            continue
+        sequence = ''
+        for repeat in sptRepeats:
+            if repeat not in repeatsDict:
+                print("Unrecoginized repeat in spatype " + repeat + ", found in line " + str(line + 1))
+            sequence += repeatsDict[repeat]
+        outfile.write('>' + name + '\n' + sequence + '\n')