Merge pull request #19 from tkonopka/lowercase

support for reference sequences with lowercase characters (a, c, g, t)
parklab · Nov 8, 2024 · b95f02d · b95f02d
2 parents a9c219d + b09fa76
commit b95f02d
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Showing 3 changed files with 17 additions and 5 deletions.
diff --git a/src/bamsnap.egg-info/SOURCES.txt b/src/bamsnap.egg-info/SOURCES.txt
@@ -1,6 +1,5 @@
 MANIFEST.in
 README.md
-setup.cfg
 setup.py
 src/bamsnap/__init__.py
 src/bamsnap/_logging.py

diff --git a/src/bamsnap/conf.py b/src/bamsnap/conf.py
@@ -6,19 +6,31 @@
 COLOR = {}
 COLOR['cov'] = ImageColor.getrgb("#AAAAAA")
 COLOR['A'] = ImageColor.getrgb("#00ff00")
+COLOR['a'] = ImageColor.getrgb("#00ff00")
 COLOR['T'] = ImageColor.getrgb("#ff0000")
+COLOR['t'] = ImageColor.getrgb("#ff0000")
 COLOR['G'] = ImageColor.getrgb("#d17105")
+COLOR['g'] = ImageColor.getrgb("#d17105")
 COLOR['C'] = ImageColor.getrgb("#0000ff")
+COLOR['c'] = ImageColor.getrgb("#0000ff")
 COLOR['N'] = ImageColor.getrgb("#AAAAAA")
 COLOR['wA'] = ImageColor.getrgb("#64E464")
+COLOR['wa'] = ImageColor.getrgb("#64E464")
 COLOR['wG'] = ImageColor.getrgb("#CAB7A1")
+COLOR['wg'] = ImageColor.getrgb("#CAB7A1")
 COLOR['wC'] = ImageColor.getrgb("#8C8CD9")
+COLOR['wc'] = ImageColor.getrgb("#8C8CD9")
 COLOR['wT'] = ImageColor.getrgb("#DE7878")
+COLOR['wt'] = ImageColor.getrgb("#DE7878")
 COLOR['wN'] = ImageColor.getrgb("#AAAAAA")
 COLOR['dA'] = ImageColor.getrgb("#078c07")
+COLOR['da'] = ImageColor.getrgb("#078c07")
 COLOR['dT'] = ImageColor.getrgb("#9c0808")
+COLOR['dt'] = ImageColor.getrgb("#9c0808")
 COLOR['dG'] = ImageColor.getrgb("#995508")
+COLOR['dg'] = ImageColor.getrgb("#995508")
 COLOR['dC'] = ImageColor.getrgb("#060680")
+COLOR['dc'] = ImageColor.getrgb("#060680")
 COLOR['dN'] = ImageColor.getrgb("#5c5959")
 COLOR['MAPQ_0'] = ImageColor.getrgb("#EFEFEF")
 COLOR['READ'] = ImageColor.getrgb("#c8c8c8")

diff --git a/src/bamsnap/drawreadset.py b/src/bamsnap/drawreadset.py
@@ -28,10 +28,11 @@ def get_image(self, w, h, bgcolor="FFFFFF"):
 
     def get_vaf(self, base_composition, dp, posi, refseq):
         aflist = []
-        for b1 in base_composition.keys():
-            if refseq[posi] != b1:
-                aflist.append(base_composition[b1]/dp)
-        return max(aflist)
+        ref_base = str(refseq[posi]).upper()
+        for b1, v1 in base_composition.items():
+            if ref_base != b1:
+                aflist.append(v1/dp)
+        return max(aflist, default=0.0)
 
     def draw_coverage(self, dr, w, h):
         try: