proviral_landscape_plot: handle HIVIntact error codes

alldata/bblab_site/tools/proviral_landscape_plot/proviral_landscape_plot.py

@@ -15,34 +15,56 @@
                    'Premature Stop': "#CC6677",
                    'Chimera': "#AA4499",
                    'Scrambled': "#882255",
+                   'Large Insertion': "#DDCC77",
+                   'Frameshift': "#DDAA77",
+                   'Divergence': "#661100",
                    }
+
 # colors are chosen from Paul Tol's muted color scheme, which is color-blind safe
 # if another defect color is needed, this one is recommended: #DDCC77
 HIGHLIGHT_COLORS = {'Defect Region': "black",
                     'Inverted Region': "#AFAFAF",
                     }
+
 DEFECT_TYPE = {'LargeDeletion': 'Large Deletion',
+               'LongDeletion': 'Large Deletion',
                'InternalInversion': 'Inversion',
                'ScramblePlus': 'Scrambled',
                'ScrambleMinus': 'Scrambled',
                'ScrambleCheck': 'Scrambled',
+               'Scramble': 'Scrambled',
                'Hypermut': 'Hypermutated',
+               'APOBECHypermutation': 'Hypermutated',
                'Intact': 'Intact',
                'Inferred_Intact': 'Intact',
                'PrematureStop_OR_AAtooLong_OR_AAtooShort': 'Premature Stop',
                'PrematureStop_OR_AAtooLong_OR_AAtooShort_GagNoATG': 'Premature Stop',
                'Inferred_PrematureStopORInframeDEL': 'Premature Stop',
                'Inferred_PrematureStopORInframeDEL_GagNoATGandFailed': 'Premature Stop',
                'Inferred_PrematureStopORInframeDEL_GagNoATG': 'Premature Stop',
+               'InternalStop': "Premature Stop",
+               'MutatedStopCodon': "Premature Stop",
+               'MutatedStartCodon': "Premature Stop",
+               'SequenceDivergence': "Divergence",
+               'Deletion': "Premature Stop",
+               'Insertion': "Large Insertion",
+               'Frameshift': "Frameshift",
                '5DEFECT': "5' Defect",
                '5DFECT_IntoGag': "5' Defect",  # this is a typo in HIVSeqinR
                '5DEFECT_GagNoATGGagPassed': "5' Defect",
                '5DEFECT_GagNoATGGagFailed': "5' Defect",
                'Inferred_Intact_GagNoATG': "5' Defect",
                'Inferred_Intact_NoGag': "5' Defect",
                'Intact_GagNoATG': "5' Defect",
+               'MajorSpliceDonorSiteMutated': "5' Defect",
+               'PackagingSignalDeletion': "5' Defect",
+               'PackagingSignalNotComplete': "5' Defect",
+               'RevResponseElementDeletion': "5' Defect",
                'NonHIV': 'Chimera',
+               'AlignmentFailed': 'Chimera',
+               'UnknownNucleotide': 'Chimera',
                }
+
 # There are some defects where we don't care about the alignment and just want to plot lines:
 LINE_DEFECTS = ['Hypermutated', 'Intact', 'Premature Stop']
 DEFECT_ORDER = {'Intact': 10,
@@ -51,9 +73,12 @@
                 'Large Deletion': 40,
                 'Inversion': 50,
                 'Premature Stop': 60,
+                'Large Insertion': 63,
+                'Frameshift': 67,
                 'Scrambled': 70,
                 'Chimera': 80,
                 }
+
 START_POS = 638
 END_POS = 9632
 LEFT_PRIMER_END = 666
@@ -159,12 +184,13 @@ def add_sidebar(self, sidebar_x, sidebar_ystart, fontsize, drawing):
             except KeyError:
                 print(f"No color defined for defect {defect}")
                 continue
+
             # percentage sidebar
             sidebar_height = self.defect_percentages[defect] / 100 * (self.lineheight + 1) * self.num_samples
             sidebar_label = f'{round(self.defect_percentages[defect], 1)}%'
             sidebar_ystart -= sidebar_height
             sidebar_label_y = fontsize / 4 + sidebar_ystart + 0.5 * sidebar_height
-            if self.defect_percentages[defect] < 3:
+            if self.defect_percentages[defect] < 0.1:
                 # skip very small percentages
                 pending_percentages.append((self.defect_percentages[defect], sidebar_height, color))
             else:
@@ -235,12 +261,14 @@ def __init__(self, figure, tot_samples):
         self.figure = figure
         self.curr_multitrack = []
         self.tot_samples = tot_samples
-        self.lineheight = 500 / self.tot_samples
+        self.lineheight = 500 / self.tot_samples if self.tot_samples > 0 else 0
         if self.lineheight > 5:
             self.lineheight = 5
         self.xaxisheight = 0
 
     def add_line(self, samp_name, xstart, xend, defect_type, highlight):
+        highlight = None
+
         is_first = False
         if defect_type not in DEFECT_TO_COLOR.keys():
             print(f"Unknown defect: {defect_type}")
@@ -294,7 +322,8 @@ def make_gene_track(self, xstart, xend, defect_type, highlight=False):
 
     def draw_current_multitrack(self):
         # draw line and reset multitrack
-        self.figure.add(Multitrack(self.curr_multitrack), gap=1)
+        if self.curr_multitrack:
+            self.figure.add(Multitrack(self.curr_multitrack), gap=1)
         self.curr_multitrack = []
 
     def add_xaxis(self):