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| 1 | + | # -*- coding: cp1252 -*- |
| 2 | ||
| 3 | import csv | |
| 4 | from itertools import izip | |
| 5 | import time | |
| 6 | import shutil | |
| 7 | import os | |
| 8 | from Bio import SeqIO | |
| 9 | ||
| 10 | import wx | |
| 11 | import wx.grid as gridlib | |
| 12 | import wx.lib.printout as printout | |
| 13 | import wx.aui as aui | |
| 14 | import wx.lib.scrolledpanel as scrolled | |
| 15 | ||
| 16 | import numpy as np | |
| 17 | import matplotlib | |
| 18 | from matplotlib.figure import Figure | |
| 19 | from matplotlib.backends.backend_wxagg import FigureCanvasWxAgg as FigureCanvas | |
| 20 | import matplotlib.patches as mpatches | |
| 21 | ||
| 22 | class DrawSchema(scrolled.ScrolledPanel): | |
| 23 | """ | |
| 24 | Draw schema with matplotlib. | |
| 25 | """ | |
| 26 | def __init__(self, parent, id = -1): | |
| 27 | scrolled.ScrolledPanel.__init__(self, parent, -1) | |
| 28 | ||
| 29 | vbox = wx.BoxSizer(wx.VERTICAL) | |
| 30 | ||
| 31 | # Create figure. | |
| 32 | self.fig = matplotlib.figure.Figure(figsize=(20, 15), facecolor='white') | |
| 33 | self.axes = self.fig.add_subplot(111) | |
| 34 | # ---------------------------------------------------------------------------- | |
| 35 | # Draw sequence as line. | |
| 36 | seq_x = 0.9 | |
| 37 | seq_y = 0.95 | |
| 38 | seq_length = -1000 | |
| 39 | self.axes.annotate('', xy=(seq_x, seq_y), xycoords='data',
| |
| 40 | xytext=(seq_length, 0), textcoords='offset points', | |
| 41 | arrowprops=dict(facecolor='black', arrowstyle="-", linewidth=5), | |
| 42 | horizontalalignment='right', verticalalignment='bottom', | |
| 43 | ) | |
| 44 | # ---------------------------------------------------------------------------- | |
| 45 | # Draw primers. | |
| 46 | # x = pos of primer | |
| 47 | # x = 0 bp = 0.066 | |
| 48 | # x = 1000 bp = 0.9 | |
| 49 | # 1 bp = 0.000834 | |
| 50 | # divide primer by scaled down, because seq is scaled down | |
| 51 | # scaled down = seq_length/1000 | |
| 52 | # x = pos * 0,000834 * scaled down | |
| 53 | #--------------------------------------------------------- | |
| 54 | # primer_y = up and down in 0.05 steps | |
| 55 | primer_y = 0.9 | |
| 56 | primer_length = -70 | |
| 57 | #--------------------------------------------------------- | |
| 58 | # text_y 0.8 # 0.04 steps | |
| 59 | # 1 bp = 0.143 | |
| 60 | # 1000 bp = 0.81 | |
| 61 | # x = pos * 0,000667 * scaled down | |
| 62 | text_y = 0.8 | |
| 63 | #--------------------------------------------------------- | |
| 64 | seq_length = 2054 | |
| 65 | scale_factor = float(float(seq_length)/1000.0) | |
| 66 | ||
| 67 | data = ['ARM(BstX-Sbf)R\t-\tMySequence\t1782\tAGACATGGGAACTCGGGAAGGAGAGGCC\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\t0\t0:G>C,1:A>C,3:T>G\n', 'ARM(BstX-Spe)F\t+\tMySequence\t1786\tATGGGAACTCGGGAAGGAGATGAA\tIIIIIIIIIIIIIIIIIIIIIIII\t0\t23:G>A\n', 'ARM-203R\t-\tMySequence\t2050\tCTATCTCTTCTGCCCCTCAAAGG\tIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-50F\t+\tMySequence\t656\tTAATGATAATCTTCCTAATACCCGTCAG\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-IN442R\t-\tMySequence\t350\tGTAATCTTCCCTGGACCCCGG\tIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-OE-454F-SpeI\t+\tMySequence\t440\tCCATACTAGTCATGAGGCCTCATCGATCAGTC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\t0\t4:C>A,7:G>A\n', 'ARM-107F\t+\tMySequence\t713\tGATGATACGAGTTCCAGGTGATAGG\tIIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-163F\t+\tMySequence\t769\tTTGCTGACCGTGGGCTTTC\tIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-203R\t-\tMySequence\t787\tCTATCTCTTCTGCCCCTCAAAGG\tIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-278R\t-\tMySequence\t864\tCAGCGGCAAACATCTGACAAG\tIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-318R\t-\tMySequence\t905\tGTCGTTATCCATGGATGCCC\tIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-50F\t+\tMySequence\t656\tTAATGATAATCTTCCTAATACCCGTCAG\tIIIIIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-FL32F\t+\tMySequence\t31\tTGACCGACCAGCCACCAC\tIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-FL40F\t+\tMySequence\t39\tCAGCCACCACCAACCCAAAC\tIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-INT178-R\t-\tMySequence\t762\tGGAGAGGTTGCTGACCGTGGGC\tIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-INT473-R\t-\tMySequence\t1054\tGGATTGCCATTGCTAATTGTGGGGC\tIIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-INT489-F\t+\tMySequence\t1094\tTGGCCTTCTTCATTCACCCGATGC\tIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-INT958-R\t-\tMySequence\t1544\tGACTGCGATTGGGCAGGCGC\tIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-OE-1898R\t-\tMySequence\t1876\tGTTATTGTTGTTGACTGGCGCT\tIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-OE1898R-ApaI\t-\tMySequence\t1876\tGTTATTGTTGTTGACTGGCGCTGGGCCCTGC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\t0\t4:A>C,5:T>C,7:T>G\n', 'ARM-OE-1970R\t-\tMySequence\t1946\tCTGGTGGATTAGTTGCTGTGTTTG\tIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-OE-407F\t+\tMySequence\t406\tTGTGAACCATCCTGAAATCTGA\tIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-OE40F-SpeI\t+\tMySequence\t33\tACCGACTAGTCACCACCAACCCAAACC\tIIIIIIIIIIIIIIIIIIIIIIIIIII\t0\t6:C>T,9:C>T\n', 'ARM-OE-454F\t+\tMySequence\t453\tGAGGCCTCATCGATCAGTCTTTAG\tIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-SPepAS\t-\tMySequence\t480\tATGCAAATGGCTCTGCTAGCAAGGCTTTCTCTTGCAAGTTCTGAAGGAAGAGAGTCTGG\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\t0\t1:A>G\n', 'ARM-TS-10F\t+\tMySequence\t287\tAGCCTTCAAGATTTGAGCACCACAG\tIIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-TS-11F\t+\tMySequence\t313\tCAACAGCCTCCTACATCCTGTGTCG\tIIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-TS-12R\t-\tMySequence\t577\tCAGAACAATCAACGAAGGAAGCATTTC\tIIIIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-TS-13R\t-\tMySequence\t687\tGACGAGGAGTGTGACATCAACGATG\tIIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-TS-14R\t-\tMySequence\t350\tGTAATCTTCCCTGGACCCCGG\tIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-TS-4F\t+\tMySequence\t32\tGACCGACCAGCCACCACCAAC\tIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-TS-5R\t-\tMySequence\t246\tGTATCCGCCCCTTCCGCAAC\tIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-TS-6R\t-\tMySequence\t216\tTCCCCCTCACCGCAGCATC\tIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-TS-7R\t-\tMySequence\t49\tCAACCCAAACCAACGCGGC\tIIIIIIIIIIIIIIIIIII\t0\t\n', 'HO14H18_3UTR-F\t+\tMySequence\t1329\tAAGCCTCTCGTGGACTTGCT\tIIIIIIIIIIIIIIIIIIII\t0\t\n', 'HO14H18_3UTR-R\t-\tMySequence\t1604\tAGCGAAAGCGAAGGAAAATG\tIIIIIIIIIIIIIIIIIIII\t0\t\n', 'N-ARM1231F\t+\tMySequence\t1788\tGGGAACTCGGCGAGGAGATGATG\tIIIIIIIIIIIIIIIIIIIIIII\t0\t10:G>C,11:A>G,21:G>T\n', 'RNR5-598R\t-\tMySequence\t577\tCAGAACAATCAACGAAGGAAGCAT\tIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'RNR5_RNAi-F\t+\tMySequence\t1218\tCATGTCCTGGAAACAGGGAA\tIIIIIIIIIIIIIIIIIIII\t0\t\n', 'RNR5_RNAi-R\t-\tMySequence\t1801\tGGAGATGAGGACGATGGTCC\tIIIIIIIIIIIIIIIIIIII\t0\t\n', 'WRNR5-RACE4\t-\tMySequence\t466\tTCAGTCTTCAGATTATGCAAATGGCTCTGC\tIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\t0\t21:T>C\n', 'ARM-EXON1-F1\t+\tMySequence\t114\tGTGCCGTGCCGTGCCTCA\tIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-EXON1-F1\t+\tMySequence\t109\tGTGCCGTGCCGTGCCTCA\tIIIIIIIIIIIIIIIIII\t1\t15:G>T,16:T>C,17:G>A\n', 'ARM-EXON1-F1\t+\tMySequence\t104\tGTGCCGTGCCGTGCCTCA\tIIIIIIIIIIIIIIIIII\t1\t15:G>T,16:T>C,17:G>A\n', 'ARM-EXON1-R1\t-\tMySequence\t246\tGTATCCGCCCCTTCCGGCAA\tIIIIIIIIIIIIIIIIIIII\t0\t0:C>A,2:A>C,3:C>G\n', 'ARM-EXON2-F1\t+\tMySequence\t293\tCAAGATTTGAGCACCACAGGCAACAG\tIIIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-EXON2-R1\t-\tMySequence\t350\tGTAATCTTCCCTGGACCCCGGG\tIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'ARM-EXON2-R2\t-\tMySequence\t417\tCTGAAATCTGATGCACATGTGAACCAT\tIIIIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'WRNR5-R1\t-\tMySequence\t406\tTGTGAACCATCCTGAAATCTGATGC\tIIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'WRNR5-F1\t+\tMySequence\t403\tGCATGTGAACCATCCTGAAATCTGA\tIIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'WRNR5-R4\t-\tMySequence\t333\tTGTCGGTACTTGGTAGGGTAATCTTCC\tIIIIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'WRNR5-F4\t+\tMySequence\t216\tTTCCCCTCACCGCAGCATC\tIIIIIIIIIIIIIIIIIII\t0\t1:C>T\n', 'WRNR5-R5\t-\tMySequence\t211\tCTCGTTTCCCCTCACCGCA\tIIIIIIIIIIIIIIIIIII\t0\t12:C>T,17:C>T\n', 'WRNR5-cDNA-Seq_1670R\t-\tMySequence\t1726\tGAACACCACGCGCAAGAGAAAAG\tIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'WRNR5-cDNA-Seq_1306R\t-\tMySequence\t1363\tCACGAGGAAAGAAAGATGCGGTTA\tIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'WRNR5-cDNA-Seq_798R\t-\tMySequence\t855\tCCATCTGTTCGGCGGCAAA\tIIIIIIIIIIIIIIIIIII\t0\t8:A>G,14:T>C\n', 'WRNR5-cDNA-Seq_729R\t-\tMySequence\t786\tTCTGTCTCTTCCGCCCCTCAAA\tIIIIIIIIIIIIIIIIIIIIII\t0\t10:T>C,18:A>G\n', 'WRNR5-cDNA-Seq_530R\t-\tMySequence\t578\tGGAACAATCAACGGAGGAAGCATC\tIIIIIIIIIIIIIIIIIIIIIIII\t0\t0:T>C,10:A>G,23:A>G\n', 'WRNR5-cDNA-Seq_1714F\t+\tMySequence\t1770\tTTCCGCAGCCAAAGACAT\tIIIIIIIIIIIIIIIIII\t0\t\n', 'WRNR5-cDNA-Seq_1670F\t+\tMySequence\t1726\tGAACACCACGCGCAAGAGAAAAG\tIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'WRNR5-cDNA-Seq_1302F\t+\tMySequence\t1359\tAGCCCACGAGGAAAGAAAGATGC\tIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'WRNR5-cDNA-Seq_933F\t+\tMySequence\t990\tATAGAAGGTCAGAGATCAGCAACA\tIIIIIIIIIIIIIIIIIIIIIIII\t0\t\n', 'WRNR5-cDNA-Seq_864F\t+\tMySequence\t921\tGCCCGGGGTGATTTCTCTGC\tIIIIIIIIIIIIIIIIIIII\t0\t7:A>G\n'] | |
| 68 | ||
| 69 | for primer in data: | |
| 70 | primer = primer.strip() | |
| 71 | primer = primer.split('\t')
| |
| 72 | primer_name = primer[0] | |
| 73 | primer_pos = primer[3] | |
| 74 | orientation = primer[1] | |
| 75 | if orientation == '+': | |
| 76 | arrow = "->" | |
| 77 | colour = 'red' | |
| 78 | elif orientation == '-': | |
| 79 | arrow = "<-" | |
| 80 | colour = 'blue' | |
| 81 | ||
| 82 | # Calculate primer and text position | |
| 83 | primer_x = (float(primer_pos) / scale_factor) * 0.000834 | |
| 84 | text_x = (float(primer_pos) / scale_factor) * 0.000667 | |
| 85 | ||
| 86 | self.axes.annotate('', xy=(primer_x+0.06, primer_y), xycoords='data',
| |
| 87 | xytext=(primer_length, -0.1), textcoords='offset points', # -50 = length, 0= direction | |
| 88 | arrowprops=dict(edgecolor=colour, arrowstyle=arrow, linewidth=3), | |
| 89 | horizontalalignment='right', verticalalignment='bottom', | |
| 90 | ) | |
| 91 | ||
| 92 | self.fig.text(text_x+0.15, text_y, primer_name + ' (' + str(primer_pos) + ')', ha="center", size=14)
| |
| 93 | ||
| 94 | primer_y = primer_y - 0.05 | |
| 95 | text_y = text_y - 0.04 | |
| 96 | ||
| 97 | # ---------------------------------------------------------------------------- | |
| 98 | # Description | |
| 99 | self.fig.text(0.186, 0.97, 'Primer Factory 2 Results', ha="center", size=14) | |
| 100 | self.fig.text(0.189, 0.95, str(time.ctime()), ha="center", size=14) | |
| 101 | self.fig.text(0.189, 0.93, 'Query Sequence ' + str(seq_length) +' bp', ha="center", size=14) | |
| 102 | self.fig.text(0.185, 0.91, str(len(data)) +' Primers where found', ha="center", size=14) | |
| 103 | # Scale | |
| 104 | self.fig.text(0.14, 0.87, '0 bp', ha="center", size=14) | |
| 105 | self.fig.text(0.805, 0.87, str(seq_length) +' bp', ha="center", size=14) | |
| 106 | ||
| 107 | self.axes.set_frame_on(False) | |
| 108 | self.axes.set_axis_off() | |
| 109 | ||
| 110 | self.canvas = FigureCanvas(self, -1, self.fig) | |
| 111 | ||
| 112 | vbox.Add(self.canvas, 0, wx.ALIGN_LEFT|wx.ALL, 5) | |
| 113 | self.SetSizer(vbox) | |
| 114 | self.SetAutoLayout(1) | |
| 115 | self.SetupScrolling() | |
| 116 | ||
| 117 | ||
| 118 | ||
| 119 | class ShowResults(wx.Frame): | |
| 120 | def __init__(self): | |
| 121 | wx.Frame.__init__(self, None, wx.ID_ANY, | |
| 122 | "Primer Factory Results", | |
| 123 | size=(1350,1000)) | |
| 124 | ||
| 125 | self._mgr = aui.AuiManager() | |
| 126 | ||
| 127 | self._mgr.SetManagedWindow(self) | |
| 128 | ||
| 129 | self.notebook = aui.AuiNotebook(self, wx.aui.AUI_NB_SCROLL_BUTTONS) | |
| 130 | panelTwo = DrawSchema(self.notebook) | |
| 131 | ||
| 132 | self.notebook.AddPage(panelTwo, "Schema", False) | |
| 133 | ||
| 134 | self._mgr.AddPane(self.notebook, | |
| 135 | aui.AuiPaneInfo().Name("notebook_content").
| |
| 136 | CenterPane().PaneBorder(False)) | |
| 137 | self._mgr.Update() | |
| 138 | ||
| 139 | ||
| 140 | if __name__ == '__main__': | |
| 141 | app = wx.PySimpleApp() | |
| 142 | frame = ShowResults() | |
| 143 | frame.Show(True) | |
| 144 | app.MainLoop() |
