split-from-imgt.py: More robust sequence comparison

We need to ignore case as well as dots that can be introduced by
gapped sequences as well as comments that may be introduced by
missing Phe.

germline/split-from-imgt.py

@@ -114,7 +114,11 @@ def check_imgt_ncbi_consistency(imgt_info, imgt_data, ncbi_target, ncbi_start, n
         # Check that sequences are identical
         ncbi_seq = ncbi.get_gene_sequence(ncbi_target, '', ncbi_start, ncbi_end, 0).split('\n')[1:]
         gene_lines = imgt_data.split('\n')[1:]
-        if ncbi_seq != gene_lines:
+        if gene_lines[0].startswith('#'):
+            gene_lines = gene_lines[1:]
+        imgt_seq = ''.join(gene_lines).upper().replace('.', '')
+        ncbi_seq = ''.join(ncbi_seq).upper()
+        if imgt_seq != ncbi_seq:
             print"WARNING: Sequences for %s differ between IMGT and NCBI:\n%s\n%s" % (imgt_info['imgt_name'], ''.join(gene_lines), ''.join(ncbi_seq))
 
 def store_data_if_updownstream(fasta_header, path, data, genes):