feat(pretty print): breaking up creation of each line in display into…

… subclasses

src/hgvs/pretty/renderer/chrom_seq_renderer.py

@@ -0,0 +1,37 @@
+from hgvs.pretty.models import VariantData
+from hgvs.pretty.renderer.renderer import BasicRenderer
+
+
+class ChromSeqRendered(BasicRenderer):
+
+    def legend(self)->str:
+        return "seq    -> : "
+
+    def display(self, data:VariantData)->str:
+        """colors the ref sequences with adenine (A, green), thymine (T, red), cytosine (C, yellow), and guanine (G, blue)"""
+        from hgvs.pretty_print import ENDC, TBLUE, TGREEN, TRED, TYELLOW
+
+        var_seq = ""
+        for p in data.position_details:
+            c = p.ref
+
+            if not c:
+                var_seq += "."
+                continue
+
+            if self.config.useColor:
+                if c == "A":
+                    var_seq += TGREEN
+                elif c == "T":
+                    var_seq += TRED
+                elif c == "C":
+                    var_seq += TYELLOW
+                elif c == "G":
+                    var_seq += TBLUE
+
+            var_seq += c
+
+            if self.config.useColor:
+                var_seq += ENDC
+
+        return var_seq

src/hgvs/pretty/renderer/pos_info.py

@@ -0,0 +1,33 @@
+from hgvs.pretty.models import VariantData
+from hgvs.pretty.renderer.renderer import BasicRenderer
+
+
+class ChrPositionInfo(BasicRenderer):
+
+    def legend(self):
+        return "          : "
+
+    def display(self, data: VariantData) -> str:
+
+        count = -1
+        var_seq = ""
+        for pdata in data.position_details:
+            count += 1
+            g = pdata.chromosome_pos
+
+            total_chars = len(var_seq)
+
+            if total_chars > count:
+                continue
+
+            if not g:
+                var_seq += " "
+                continue
+
+            if g % 10 == 0:
+                var_seq += f"{g:,} "
+
+            else:
+                var_seq += " "
+
+        return var_seq.rstrip()

src/hgvs/pretty/renderer/prot_seq_renderer.py

@@ -0,0 +1,75 @@
+from hgvs.pretty.models import VariantData
+from hgvs.pretty.renderer.renderer import BasicRenderer
+
+
+class ProtSeqRenderer(BasicRenderer):
+
+    def legend(self):
+        legend = "aa seq -> : "
+        if self.orientation < 0:
+            legend = "aa seq <- : "
+        return legend
+
+    def display(self, data: VariantData) -> str:
+        if not data.var_c_or_n:
+            return ""
+
+        from hgvs.pretty_print import ENDC, TGREEN, TRED
+
+        var_str = ""
+        for pdata in data.position_details:
+
+            p = pdata.chromosome_pos
+
+            if not pdata.mapped_pos:
+                var_str += " "
+                continue
+
+            ref_base = pdata.ref
+
+            c_interval = pdata.c_interval
+            if not c_interval:
+                var_str += " "
+                continue
+
+            cig = pdata.cigar_ref
+            c_offset = pdata.c_offset
+            if cig == "N" or c_offset != 0:
+                var_str += " "
+                continue
+
+            if cig == "I":
+                var_str += "-"
+                continue
+
+            if not ref_base or pdata.tx:
+                ref_base = pdata.tx
+
+            protein_data = pdata.protein_data
+
+            if not protein_data:
+                var_str += " "
+                continue
+
+            aa_char = protein_data.aa_char
+
+            # color init met and stop codon if using color:
+            if protein_data.is_init_met:
+                if self.config.useColor:
+                    aa_char = TGREEN + aa_char + ENDC
+                var_str += aa_char
+                continue
+            if protein_data.is_stop_codon:
+                if self.config.useColor:
+                    aa_char = TRED + aa_char + ENDC
+                var_str += aa_char
+                continue
+
+            if not protein_data.var_p.posedit:
+                var_str += " "
+                continue
+
+            var_str += aa_char
+            continue
+
+        return var_str

src/hgvs/pretty/renderer/renderer.py

@@ -0,0 +1,14 @@
+from abc import ABC, abstractmethod
+
+class BasicRenderer(ABC):
+    def __init__(self, config, orientation:int):
+        self.config = config
+        self.orientation = orientation
+
+    @abstractmethod
+    def legend(self):
+        pass
+
+    @abstractmethod
+    def display(self):
+        pass

src/hgvs/pretty/renderer/ruler.py

@@ -0,0 +1,31 @@
+from hgvs.pretty.models import VariantData
+from hgvs.pretty.renderer.renderer import BasicRenderer
+
+
+class ChrRuler(BasicRenderer):
+
+    def legend(self):
+        """ returns the legend for this category of display"""
+        return "chrom pos : "
+
+    def display(self, data: VariantData) -> str:
+        """Draw a position indicator that diplays | every 10 bases and a . every 5
+
+        seq_start/end in interbase
+        """
+
+        ruler = ""
+
+        for pd in data.position_details:
+            p = pd.chromosome_pos
+            if not p:
+                ruler += "_"
+                continue
+
+            if p % 10 == 0:
+                ruler += "|"
+            elif p % 5 == 0:
+                ruler += "."
+            else:
+                ruler += " "
+        return ruler

src/hgvs/pretty/renderer/shuffled_variant.py

@@ -0,0 +1,93 @@
+
+
+from hgvs.pretty.models import VariantCoords, VariantData
+from hgvs.pretty.renderer.renderer import BasicRenderer
+from hgvs.sequencevariant import SequenceVariant
+
+
+class ShuffledVariant(BasicRenderer):
+
+    def __init__(self, config, orientation:int, var_g: SequenceVariant, vc: VariantCoords)->None:
+        super().__init__(config, orientation)  
+
+        self.var_g = var_g
+        self.vc = vc
+
+    def legend(self
+    ) ->str:
+
+        return "region    : "
+
+    def display(
+        self, data: VariantData
+    ) -> str:
+
+        from hgvs.pretty_print import ENDC, TBLUE, TGREEN, TRED, TYELLOW
+
+        seq_start = data.display_start
+        seq_end = data.display_end
+
+        split_char = "|"
+
+        start = self.vc.start
+        end = self.vc.end
+
+        # map interbase coordinates to 1-based display coords:
+        start = start + 1
+
+        if self.var_g.posedit.edit.type == "sub":
+            end = start
+            if len(self.vc.alt) == 1:
+                split_char = self.vc.alt
+        l = end - start + 1
+        if self.var_g.posedit.edit.type == "ins" and l == 0:
+            start = start - 1
+            end = end + 1
+            split_char = "^"
+
+        if self.var_g.posedit.edit.type == "del":
+            split_char = ""
+            if self.config.useColor:
+                split_char = TRED
+            split_char += "x"
+            if self.config.useColor:
+                split_char += ENDC
+
+        elif self.var_g.posedit.edit.type == "identity":
+            split_char = "="
+        # print(l,start, end , vc)
+
+        if start < seq_start:
+            # raise ValueError(f"Can't create shuffled representation, since start {start} < seq_start {seq_start} ")
+            return ""
+        if end > seq_end:
+            return ""
+            # raise ValueError(f"Can't create shuffled representation, since end {end} > seq_end {seq_end} ")
+
+        var_str = ""
+        in_range = False
+        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:
+                var_str += split_char
+                in_range = True
+            elif p == end:
+                var_str += split_char
+                in_range = False
+            elif p > end and in_range:
+                in_range = False
+                var_str += " "
+            elif in_range:
+                var_str += "-"
+            else:
+                var_str += " "
+
+        return var_str

src/hgvs/pretty/renderer/tx_alig_renderer.py

@@ -0,0 +1,96 @@
+import math
+from hgvs.pretty.models import VariantData
+from hgvs.pretty.renderer.renderer import BasicRenderer
+
+
+class TxAligRenderer(BasicRenderer):
+
+    def legend(self)->str:
+        orientation = "->"
+        if self.orientation < 0:
+            orientation = "<-"
+        return f"tx seq {orientation} : "
+
+
+    def display(self, data: VariantData) -> str:
+        """If transcript info is available show the details of the tx for the region."""
+        if not data.var_c_or_n:
+            return ""
+
+        from hgvs.pretty_print import ENDC, TYELLOW, TPURPLE
+        var_str = ""
+
+        first_c = None
+        last_c = None
+
+        coding = False
+        c_pos = None
+
+        counter = -1
+        for pdata in data.position_details:
+
+            counter += 1
+
+            if not pdata.mapped_pos:
+                var_str += " "
+                continue
+
+
+            n_pos = pdata.n_pos
+            c_pos = pdata.c_pos
+            cig = pdata.cigar_ref
+            c_offset = pdata.c_offset
+
+            if cig == "N" or (c_offset is not None and c_offset != 0):
+                coding = False
+                var_str += " "
+                continue
+
+
+            if c_pos:                
+                # if we get here we are coding...
+                last_c = f"c.{c_pos}"
+            else:
+                last_c = f"n.{n_pos}"
+                c_pos = n_pos
+            if not coding:
+
+                if not first_c:
+                    first_c = last_c
+
+                coding = True
+
+            if cig == "=":
+                #c3 = (c_pos - 1) % 3
+                if c_pos:
+                    bg_col = math.ceil(c_pos / 3) % 2
+                elif n_pos:
+                    bg_col = math.ceil(n_pos / 3) % 2
+                else:
+                    var_str += " "
+                    continue
+
+                # print(p, c_pos, c3, bg_col )
+                if n_pos >= 0:
+                    base = pdata.tx
+                    if self.config.useColor and c_pos > 0:
+                        if bg_col:
+                            var_str += TPURPLE + base + ENDC
+                        else:
+                            var_str += TYELLOW + base + ENDC
+                    else:
+                        if c_pos is None or c_pos < 0:
+                            var_str += base.lower()
+                        else:
+                            var_str += base
+                    continue
+
+            elif cig == "X" or cig == "D":
+                # for mismatches and tx-insertions show sequence
+                var_str += pdata.tx
+                continue
+
+            else:
+                var_str += "-"
+
+        return var_str