Several documented tweaks for recent issues, see VV code changes and …

…issues
openvar · Sep 12, 2022 · a8a18a1 · a8a18a1
1 parent a2599f5
commit a8a18a1
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Showing 3 changed files with 11 additions and 8 deletions.
diff --git a/VariantFormatter/formatter.py b/VariantFormatter/formatter.py
@@ -306,7 +306,6 @@ def remove_reference(hgvs_nucleotide):
 
 
 def gap_checker(hgvs_transcript, hgvs_genomic, genome_build, vfo):
-
     tx_id = hgvs_transcript.ac
     if re.match('ENST', tx_id):
         hn = vfo.genebuild_normalizer

diff --git a/VariantFormatter/gapGenes.py b/VariantFormatter/gapGenes.py
@@ -50,7 +50,6 @@ def compensate_g_to_t(hgvs_tx,
                                         vm, vfo)
         hgvs_tx_returns = [normalized_tx, False, None, None, None]
 
-
     else:
         gene_symbol = hdp.get_tx_identity_info(hgvs_tx.ac)[6]
 
@@ -102,6 +101,7 @@ def compensate_g_to_t(hgvs_tx,
                                                                                                          nw_rel_var[0],
                                                                                                          "")
 
+
             # Populate output list
             gap_compensated_tx_2 = [nw_rel_var[0]]
             if "does not represent a true variant" in data["gapped_alignment_warning"] \
@@ -162,6 +162,7 @@ def fully_normalize(hgvs_tx, hgvs_genomic, hn, reverse_normalizer, vm, vfo):
     # Obtain the orientation of the transcript wrt selected genomic accession
     exon_alignments = vfo.tx_exons(tx_id, hgvs_genomic.ac, alt_aln_method)
     orientation = int(exon_alignments[0]['alt_strand'])
+
     # Normalize the genomic variant 5 prime if antisense or 3 prime if sense
     if orientation == -1:
         hgvs_genomic = rhn.normalize(hgvs_genomic)

diff --git a/VariantFormatter/variantformatter.py b/VariantFormatter/variantformatter.py
@@ -13,13 +13,8 @@
 import collections
 import copy
 import vvhgvs.exceptions
-
-# import VF
 import VariantFormatter.formatter as formatter
-# import VV
 import VariantValidator.modules.liftover as lo
-import VariantValidator.modules.gapped_mapping
-from VariantValidator.modules.variant import Variant
 
 
 # Custom Exceptions
@@ -348,7 +343,7 @@ def __init__(self, variant_description, genome_build, vfo, transcript_model=None
             tx_id = tx_alignment_data[0]
             hgvs_transcript_dict = formatter.hgvs_genomic2hgvs_transcript(g_hgvs, tx_id, self.vfo)
 
-            # Gap checking            
+            # Gap checking
             try:
                 am_i_gapped = formatter.gap_checker(hgvs_transcript_dict['hgvs_transcript'], g_hgvs,
                                                     self.genome_build, self.vfo)
@@ -456,6 +451,14 @@ def __init__(self, variant_description, genome_build, vfo, transcript_model=None
                                                specified_tx_variant=specified_tx_variant
                                                )
 
+                    if "am_i_gapped" in current_lift.keys():
+                        if order_my_tp['gapped_alignment_warning'] is "":
+                            order_my_tp['gapped_alignment_warning'] = current_lift['am_i_gapped'][
+                                'gapped_alignment_warning']
+                        if order_my_tp['gap_statement'] is "":
+                            order_my_tp['gap_statement'] = current_lift['am_i_gapped']['gap_position']
+                        current_lift.pop("am_i_gapped")
+
                     if g_to_g_lift == {}:
                         g_to_g_lift = current_lift