feat(reverse-strand): Now showing reverse strand transcript in 5'-3' …

…orientation relative to the transcript by default (can be configured).

src/hgvs/pretty/console/chrom_seq_renderer.py

@@ -5,7 +5,13 @@
 class ChromSeqRendered(BasicRenderer):
 
     def legend(self) -> str:
-        return "seq    -> : "
+
+        if self.orientation < 0 and self.config.reverse_display:
+            arrow = '<-'
+        else:
+            arrow = '->'
+
+        return f"seq    {arrow} : "
 
     def display(self, data: VariantData) -> str:
         """colors the ref sequences with adenine (A, green), thymine (T, red), cytosine (C, yellow), and guanine (G, blue)"""

src/hgvs/pretty/console/chrom_seq_reverse_renderer.py

@@ -7,7 +7,12 @@
 class ChromReverseSeqRendered(BasicRenderer):
 
     def legend(self) -> str:
-        return "seq    <- : "
+        if self.orientation < 0 and self.config.reverse_display:
+            arrow = '->'
+        else:
+            arrow = '<-'
+
+        return f"seq    {arrow} : "
 
     def display(self, data: VariantData) -> str:
         """colors the ref sequences with adenine (A, green), thymine (T, red), cytosine (C, yellow), and guanine (G, blue)"""

src/hgvs/pretty/console/prot_seq_renderer.py

@@ -5,10 +5,15 @@
 class ProtSeqRenderer(BasicRenderer):
 
     def legend(self):
-        legend = "aa seq -> : "
-        if self.orientation < 0:
-            legend = "aa seq <- : "
-        return legend
+
+        if self.orientation > 0:
+            arrow = "->"
+        elif self.orientation < 0 and self.config.reverse_display:
+            arrow = "->"
+        else:
+            arrow = "<-"
+
+        return f"aa seq {arrow} : "
 
     def display(self, data: VariantData) -> str:
         if not data.var_c_or_n:
@@ -19,8 +24,6 @@ def display(self, data: VariantData) -> str:
         var_str = ""
         for pdata in data.position_details:
 
-            p = pdata.chromosome_pos
-
             if not pdata.mapped_pos:
                 var_str += " "
                 continue

src/hgvs/pretty/console/shuffled_variant.py

@@ -1,3 +1,4 @@
+from logging import info
 from hgvs.pretty.models import VariantCoords, VariantData
 from hgvs.pretty.console.renderer import BasicRenderer
 from hgvs.sequencevariant import SequenceVariant
@@ -61,23 +62,36 @@ def display(self, data: VariantData) -> str:
 
         var_str = ""
         in_range = False
+
+        reverse_display = False
+        if self.orientation < 0 and self.config.reverse_display:
+            reverse_display = True        
+
         for pdata in data.position_details:
             p = pdata.chromosome_pos
-
             if not p:
                 if in_range:
                     var_str += "-"
                 else:
                     var_str += " "
                 continue
 
-            if p == start:
+            if not reverse_display and p == start:
+                var_str += split_char
+                in_range = True
+            elif reverse_display and p == end:
                 var_str += split_char
                 in_range = True
-            elif p == end:
+            elif not reverse_display and p == end:
                 var_str += split_char
                 in_range = False
-            elif p > end and in_range:
+            elif reverse_display and p == start:
+                var_str += split_char
+                in_range = False
+            elif not reverse_display and p > end and in_range:
+                in_range = False
+                var_str += " "
+            elif reverse_display and p < start and in_range:
                 in_range = False
                 var_str += " "
             elif in_range:

src/hgvs/pretty/console/tx_alig_renderer.py

@@ -7,8 +7,11 @@
 class TxAligRenderer(BasicRenderer):
 
     def legend(self) -> str:
-        orientation = "->"
-        if self.orientation < 0:
+        if self.orientation > 0:
+            orientation = "->"
+        elif self.orientation < 0 and self.config.reverse_display:
+            orientation = "->"
+        else:
             orientation = "<-"
         return f"tx seq {orientation} : "
 

src/hgvs/pretty/console/tx_ref_disagree_renderer.py

@@ -17,10 +17,8 @@ def display(self, data: VariantData) -> str:
         from hgvs.pretty.console.constants import ENDC, TRED
 
         var_str = ""
-        counter = -1
-        for p in range(data.display_start + 1, data.display_end + 1):
-            counter += 1
-            pdata = data.position_details[counter]
+
+        for pdata in data.position_details:            
             c_offset = pdata.c_offset
             if not pdata.mapped_pos:
                 var_str += " "

src/hgvs/pretty/datacompiler.py

@@ -152,7 +152,7 @@ def _get_prot_alt(
         c_pos = int(c_interval.start.base) - 1
         c3 = (c_pos) % 3
         aa_char = tlc[c3]
-        if strand < 0:
+        if strand < 0 and not self.config.reverse_display:
             aa_char = tlc[2 - c3]
 
         return ProteinData(c_pos, aa, tlc, aa_char, var_p, is_init_met, is_stop_codon, aa_index)
@@ -347,6 +347,10 @@ def data(
 
         strand = mapper.strand if mapper else 1
 
+        if strand < 0 and self.config.reverse_display:
+            pd = reversed(position_details)
+            position_details = list(pd)
+
         vd = VariantData(
             seq_start,
             seq_end,

src/hgvs/pretty/models.py

@@ -109,3 +109,4 @@ class PrettyConfig:
     all: bool = False  # print all possible hgvs_c (for all UTA transcripts)
     show_reverse_strand: bool = False  # show the reverse strand sequence for the chromosome
     alt_aln_method:str = 'splign'
+    reverse_display:bool = True # display reverse strand as the main strand (5'->3')

src/hgvs/pretty/pretty_print.py

@@ -21,8 +21,6 @@
 from hgvs.sequencevariant import SequenceVariant
 
 
-
-
 class PrettyPrint:
     """A class that provides a pretty display of the genomic context of a variant."""
 
@@ -37,7 +35,8 @@ def __init__(
         infer_hgvs_c=True,
         all=False,
         show_reverse_strand=False,
-        alt_aln_method='splign'
+        alt_aln_method='splign',
+        reverse_display = True
     ):
         """
         :param hdp: HGVS Data Provider Interface-compliant instance
@@ -60,7 +59,8 @@ def __init__(
             infer_hgvs_c,
             all,
             show_reverse_strand,
-            alt_aln_method
+            alt_aln_method,
+            reverse_display
         )
 
     def _get_assembly_mapper(self) -> AssemblyMapper:
@@ -213,7 +213,9 @@ def create_repre(
 
         renderer_cls = [ChrPositionInfo, ChrRuler, ChromSeqRendered]
 
-        if self.config.show_reverse_strand:
+        # if we show reverse strand transcripts in forward facing orientation, always
+        # show both forward and reverse strand sequences.
+        if self.config.show_reverse_strand or self.config.reverse_display and data.strand < 0:
             renderer_cls.append(ChromReverseSeqRendered)
 
         renderer_cls.append(TxRefDisagreeRenderer)
@@ -249,7 +251,6 @@ def create_repre(
                 self.config, data.strand, var_g, fully_justified_var
             )
             fully_justified_str = fully_justified_renderer.display(data)
-
             if self.config.showAllShuffleableRegions:
                 var_str += shuffled_seq_header + left_shuffled_str + "\n"
                 var_str += shuffled_seq_header + right_shuffled_str + "\n"

tests/test_pretty_print.py

@@ -17,6 +17,7 @@ def setUpClass(cls):
         cls.hdp = hgvs.dataproviders.uta.connect(mode=None, cache=None)
         cls.pp = PrettyPrint(
             cls.hdp,
+            reverse_display=False
         )
         cls.pp.useColor = False
 
@@ -87,11 +88,39 @@ def test_var_c1_reverse(self):
         for r, e in zip(result, expected_str):
             self.assertEqual(e, r)
 
+    def test_var_c1_reverse_flipped_display(self):
+        """ test the reversed display on <- strand"""
+        hgvs_c = "NM_001177507.2:c.1="
+        var_c = self.hp.parse(hgvs_c)
+
+        pp = PrettyPrint(self.hdp, show_reverse_strand=True, reverse_display=True)
+        result = pp.display(var_c)
+        print(result)
+        result = result.split("\n")
+        expected_str = (
+            "hgvs_g    : NC_000007.13:g.36763753=\n" +
+            "hgvs_c    : NM_001177507.2:c.1=\n" +
+            "hgvs_p    : NP_001170978.1:p.Met1?\n" +
+            "          :    36,763,770          36,763,750\n" +
+            "chrom pos :    |    .    |    .    |    .    |    .  \n" +
+            "seq    <- : AACCCCACGTATCGAGCCTCTACGTCAGGGGGACCTTTTAG\n" +
+            "seq    -> : TTGGGGTGCATAGCTCGGAGATGCAGTCCCCCTGGAAAATC\n" +
+            "region    :                     =                    \n" +
+            "tx seq -> : ttggggtgcatagctcggagATGCAGTCCCCCTGGAAAATC\n" +
+            "tx pos    : |    .    |    .    |   .    |    .    | \n" +
+            "          : -20       -10       1        10        20\n" +
+            "aa seq -> :                     MetGlnSerProTrpLysIle\n" +
+            "aa pos    :                                 ...      \n" +
+            "          :                     1                    \n"
+        ).split("\n")
+        for r, e in zip(result, expected_str):
+            self.assertEqual(e, r)
+
     def test_var_g_substitution(self):
         hgvs_g = "NC_000007.13:g.36561662C>T"
         var_g = self.hp.parse(hgvs_g)
 
-        pp = PrettyPrint(self.hdp, show_reverse_strand=True)
+        pp = PrettyPrint(self.hdp, show_reverse_strand=True, reverse_display=False)
 
         result = pp.display(var_g)
         print(result)
@@ -132,6 +161,35 @@ def test_var_g_ins(self):
         for r, e in zip(result, expected_str):
             self.assertEqual(e, r)
 
+    def test_atta_forward(self):
+        """ the ATTA[2]>ATTA[3] variant now displayed forward facing:"""
+
+        hgvs_g = "NC_000005.10:g.123346517_123346518insATTA"
+        var_g = self.hp.parse(hgvs_g)
+        pp = PrettyPrint(self.hdp, show_reverse_strand=True, reverse_display=True)
+        result = pp.display(var_g)
+        print(result)
+        result = result.split("\n")
+        expected_str = (
+            "hgvs_g    : NC_000005.10:g.123346517_123346518insATTA\n" +
+            "hgvs_c    : NM_001166226.1:c.*1_*2insTAAT\n" +
+            "hgvs_p    : NP_001159698.1:p.?\n" +
+            "          :      123,346,540         123,346,520         123,346,500\n" +
+            "chrom pos : .    |    .    |    .    |    .    |    .    |  \n" +
+            "seq    <- : AACCGTTTTTCGTTACGGTCATTAATTATTGTAAACCTTTTCGAAATA\n" +
+            "seq    -> : TTGGCAAAAAGCAATGCCAGTAATTAATAACATTTGGAAAAGCTTTAT\n" +
+            "region    :                     |------|                    \n" +
+            "tx seq -> : TTGGCAAAAAGCAATGCCAGTAATTAATAACATTTGGAAAAGCTTTAT\n" +
+            "tx pos    :    |    .    |    .    |   |   .    |    .    | \n" +
+            "          :    2860      2870      2880         *10       *20\n" +
+            "aa seq -> : LeuAlaLysSerAsnAlaSerAsnTer                     \n" +
+            "aa pos    :       ...            |||                        \n" +
+            "          :                      960                        \n" +
+            "ref>alt   : ATTA[2]>ATTA[3]\n"
+        ).split("\n")
+        for r, e in zip(result, expected_str):
+            self.assertEqual(e, r)
+
     def test_var_g_dup(self):
         hgvs_g = "NC_000005.10:g.123346522_123346525dup"
         var_g = self.hp.parse(hgvs_g)
@@ -366,7 +424,7 @@ def test_tiny(self):
         hgvs_g = "NC_000005.10:g.123346517_123346518insATTA"
         var_g = self.hp.parse(hgvs_g)
 
-        tiny_pp = PrettyPrint(self.hdp, padding_left=0, padding_right=0)
+        tiny_pp = PrettyPrint(self.hdp, padding_left=0, padding_right=0, reverse_display=False)
 
         result = tiny_pp.display(var_g)
         print(result)
@@ -408,7 +466,7 @@ def test_hgvs_c(self):
         hgvs_c = "NM_004572.3:c.-9_12dup"
         var_c = self.hp.parse(hgvs_c)
         pp = PrettyPrint(
-            self.hdp, padding_left=10, padding_right=110, useColor=False, showLegend=False
+            self.hdp, padding_left=10, padding_right=110, useColor=False, showLegend=False, reverse_display=False
         )
         result = pp.display(var_c)
 
@@ -508,7 +566,7 @@ def test_ref_disagree_del(self):
         hgvs_c = "NM_000682.6:c.901_911del"  # a del variant
 
         var_c = self.hp.parse(hgvs_c)
-        pp = PrettyPrint(self.hdp, infer_hgvs_c=True, padding_left=30, padding_right=40)
+        pp = PrettyPrint(self.hdp, infer_hgvs_c=True, padding_left=30, padding_right=40, reverse_display=False)
         result = pp.display(var_c)
         print(result)
         result = result.split("\n")
@@ -520,7 +578,7 @@ def test_ref_disagree_del(self):
             + "          :     96,780,960          96,780,980                   96,781,000          96,781,020\n"
             + "chrom pos :     |    .    |    .    |    .    |    .  _________  |    .    |    .    |    .    |    .  \n"
             + "seq    -> : TGCCTGGGGTTCACACTCTTCCTCCTCCTCCTCCTCCTCTTC.........GGCTTCATCCTCTGGAGATGCCCCACAAACACCCTCCTTC\n"
-            + "tx ref dif:                                           DDDDDDDDD                               \n"
+            + "tx ref dif:                                           DDDDDDDDD                                        \n"
             + "region    :                               x----------x                                                 \n"
             + "tx seq <- : ACGGACCCCAAGTGTGAGAAGGAGGAGGAGGAGGAGGAGAAGGAGGAGAAGTCGAAGTAGGAGACCTCTACGGGGTGTTTGTGGGAGGAAG\n"
             + "tx pos    :   |    .    |    .    |    .    |    .    |    .    |    .    |    .    |    .    |    .   \n"
@@ -547,7 +605,7 @@ def test_ruler(self):
         """Test the ruler display option turned on."""
         hgvs_c = "NM_001111.4:c.298G>A"
         var_c = self.hp.parse(hgvs_c)
-        pp = PrettyPrint(self.hdp, showLegend=False)
+        pp = PrettyPrint(self.hdp, showLegend=False, reverse_display=False)
 
         result = pp.display(var_c)