zoom feature

plotnineseqsuite/tool.py

@@ -0,0 +1,10 @@
+from typing import List
+
+
+def extract(data: List[str], start: int = None, end: int = None) -> List[str]:
+    complete_len = len(data[0])
+    if start is None:
+        start = 0
+    if end is None:
+        end = complete_len
+    return list(map(lambda x: x[start:end], data))

tests/test_tool.py

@@ -0,0 +1,6 @@
+from plotnineseqsuite.tool import extract
+
+
+def test_extract():
+    seqs = ['TTGTGAAAGAC', 'AAGTAAACTAA', 'TAATAAACAAA', 'TAATAAACAAA', 'CTGTAAATATT', 'TAGAAAGGTAT']
+    result = extract(seqs, start=1, end=4)

tests/test_zoom.py

@@ -0,0 +1,22 @@
+from plotnine import ggplot, coord_fixed, ggtitle, theme, element_text, scale_x_continuous
+from plotnineseqsuite.align import geom_alignedSeq, theme_seq, extract
+from math import floor, ceil
+
+seqs = ['TTGTGAAAGAC', 'AAGTAAACTAA', 'TAATAAACAAA', 'TAATAAACAAA', 'CTGTAAATATT', 'TAGAAAGGTAT']
+result = extract(seqs, start=1, end=4)
+a=ggplot() + geom_alignedSeq(data=seqs) + coord_fixed() + theme_seq()+ggtitle('Completed sequences') + theme(plot_title=element_text(size=30, ha='left'))
+b=ggplot() + geom_alignedSeq(data=result) + scale_x_continuous(breaks=lambda x: range(floor(x[0]), ceil(x[1])), labels=lambda x:x+1, expand=(0,0)) + coord_fixed() + theme_seq()+ggtitle('Fragmented sequences') + theme(plot_title=element_text(size=30, ha='left'))
+a.save('Fig. complete.png')
+b.save('Fig. fragment.png')
+
+from PIL import Image
+a_pic=Image.open('Fig. complete.png')
+b_pic=Image.open('Fig. fragment.png')
+a_width = a_pic.width
+a_height = a_pic.height
+b_width = b_pic.width
+b_height = b_pic.height
+dst = Image.new('RGB', (a_width+b_width, b_height), color='white')
+dst.paste(a_pic, (0, 0))
+dst.paste(b_pic, (a_width, 0))
+dst.save('Fig. zoom.png')