REPET V4 PASTEC release

Stable version of REPET V4 incorporating PASTEC

TEannot_snakemake/scripts/Launch_NTE50.py

+from annot_pipe import NTE50
+
+def get_genome_lenght(infile):
+    with open(infile) as file:
+        cumLength = 0
+        for line in file:
+            if line[0] != ">":
+                #                cumLength += len(string.rstrip(line))
+                cumLength += len(line.rstrip())
+
+        return cumLength
+
+
+
+genome_size=get_genome_lenght(snakemake.params.genome)
+iNTE= NTE50(FileName=snakemake.input.FLC, directory=snakemake.params.dir, genomeSize=genome_size)
+iNTE.run()
+
+iNTE= NTE50(FileName=snakemake.input.FLF, directory=snakemake.params.dir, genomeSize=genome_size)
+iNTE.run()
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