diff ete_lineage_generator.py @ 11:2db72467da51 draft

"planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/ete commit 67e136d433c0d925db362342919305b46fdffecd"

--- a/ete_lineage_generator.py	Fri Nov 20 16:56:22 2020 +0000
+++ b/ete_lineage_generator.py	Thu Mar 10 14:01:44 2022 +0000
@@ -41,7 +41,14 @@
     RANK_IDX: mapping from rank names to indices (distance to root/leaf?)
     lower: use lower taxa for filling "NA"s
     """
-    lineage_taxids = ncbi.get_lineage(taxid)
+    try:
+        lineage_taxids = ncbi.get_lineage(taxid)
+    except ValueError:
+        sys.stderr.write("[%s] could not determine lineage!\n" % taxid)
+        return
+    if lineage_taxids is None:
+        sys.stderr.write("[%s] could not determine lineage!\n" % taxid)
+        return
     lineage_ranks = ncbi.get_rank(lineage_taxids)
     lineage_names = ncbi.get_taxid_translator(lineage_taxids, try_synonyms=True)
     if lower:
@@ -121,6 +128,8 @@
 with open(options.input_species_filename) as f:
     for line in f.readlines():
         line = line.strip().replace('_', ' ')
+        if line == "":
+            continue
         try:
             taxid = int(line)
         except ValueError: