Interfase Gráfica de Usuario de la librería Biopython (bioinformática)

En la  web de la librería Biopython tenemos su definición :  "Biopython es un conjunto de herramientas disponibles gratuitamente para la computación biológica escritas en Python por un equipo internacional de desarrolladores".

Existen otras librerías similares disponibles para otros lenguajes de programación: BioPerl, BioJava, BioRuby, etc

Biopython está en constante desarrollo y cada vez incluye nuevas funcionalidades, entre las que podemos mencionar: Edición/anotación de secuencias,  alineación de secuencias (en local y en la web) , filogenética, consulta de Bases de Datos en la web (NCBI, SwisProt, Entrez, GenBank,TogoWS,etc), gestión de bases de datos locales (BioSQL), acceso a programas en la web (Blast), etc.

El objeto de este proyecto es desarrollar una GUI que facilite el uso de las diferentes funcionalidades antes mencionadas, ya que por defecto para utilizar la librería debemos desarrollar scripts con las instrucciones requeridas.

Se utiliza el paquete tkinter para desarrollar la interfase gráfica.

En la versión actual de este proyecto disponemos de las siguientes opciones:

• Alineación de secuencias mediante el uso de "wrappers" a programas externos: Clustalw, ClustalO, Muscle, Prank, Probcoms.
• Conversión entre diferentes formatos de archivos de secuencias: Fasta, fastq, genbank, embl, etc.
• Acceso a Bases de Datos en la web: Entrez, SwissProt.
• Acceso a Suites de Bioinformática en la web: EMBOSS, SMS2, T-Rex, SeWeR, etc.
• Acceso a programas externos de Alineación de Secuencias Múltiples: ClustalX, AliView, etc.
• Acceso a programas de visualización de Filogenética

A continuación el script completo del proyecto:    

""" BioPython GUI JLG 31/12/2021 """ import sys, os, time import subprocess import tkinter as tk from io import StringIO from ttkthemes import ThemedTk import tkinter as tk from tkinter import ttk from tkinter import messagebox from tkinter import scrolledtext from tkinter.filedialog import askopenfilename, asksaveasfilename , askdirectory from Bio import SeqIO from Bio.Align.Applications import ClustalwCommandline from Bio.Align.Applications import ClustalOmegaCommandline from Bio.Align.Applications import MuscleCommandline from Bio.Align.Applications import PrankCommandline from Bio.Align.Applications import DialignCommandline from Bio.Align.Applications import ProbconsCommandline from Bio import AlignIO from Bio import Phylo from Bio import Entrez from Bio import ExPASy from Bio import SwissProt from Bio.ExPASy import ScanProsite import webbrowser # User Params Entrez.email = "user_email@gmail.com" PATH_FIREFOX ='C://Program Files//Mozilla Firefox//firefox.exe' # User Functions def center_window(w=1200, h=640): ws = window.winfo_screenwidth() hs = window.winfo_screenheight() x = (ws/2) - (w/2) y = (hs/2) - (h/2) - 40 window.geometry('%dx%d+%d+%d' % (w, h, x, y)) def About(): tk.messagebox.showinfo(title="About ...", message="Python Version:\n" + sys.version ) def Close(): res = messagebox.askquestion('Exit', 'Do you want to exit?') if res == 'yes': window.destroy() class CrearToolTip(object): def __init__(self,elemento,texto='Info del objeto'): self.espera = 500 self.largo = 180 self.objeto = elemento self.texto = texto self.objeto.bind("<Enter>",self.entrar) self.objeto.bind("<Leave>",self.salir) self.objeto.bind("<ButtonPress>",self.salir) self.id = None self.tw = None def entrar(self,event=None): self.asignar() def salir(self,event=None): self.liberar() self.ocultar_tip() def asignar(self): self.liberar() self.id = self.objeto.after(self.espera,self.mostrar_tip) def liberar(self): id = self.id self.id = None if id: self.objeto.after_cancel(id) def mostrar_tip(self,event=None ): x = y = 0 x,y,cx,cy = self.objeto.bbox("insert") x += self.objeto.winfo_rootx() + 25 y += self.objeto.winfo_rooty() + 20 self.tw = tk.Toplevel(self.objeto) self.tw.wm_overrideredirect(True) self.tw.wm_geometry("+%d+%d"%(x,y)) label = tk.Label(self.tw,text=self.texto,justify="left", background = "white",relief="solid",borderwidth=1, wraplength = self.largo) label.pack(ipadx=1) def ocultar_tip(self): tw = self.tw self.tw = None if tw: tw.destroy() def rClicker(e): print (e) try: def rClick_Copy(e, apnd=0): e.widget.event_generate('<Control-c>') def rClick_Cut(e): e.widget.event_generate('<Control-x>') def rClick_Paste(e): e.widget.event_generate('<Control-v>') def rClick_Select_All(e): e.widget.focus_force() e.widget.tag_add(tk.SEL, "1.0", tk.END) def rClick_Clear_All(e): e.widget.focus_force() e.widget.tag_add(tk.SEL, "1.0", tk.END) e.widget.event_generate('<Control-x>') def rClick_Clipboard(e): window.clipboard_append(e.widget.get(1.0, tk.END )) def rClick_AliView_seq(e): FileView=seq_inuse_entry.get() subprocess.run(["ExtApp\Aliview.exe", FileView]) def rClick_AliView_aln(e): FileView=os.path.splitext(seq_inuse_entry.get())[0]+'.aln' subprocess.run(["ExtApp\Aliview.exe", FileView]) def rClick_ClustalX_seq(e): FileView=seq_inuse_entry.get() subprocess.run(["ExtApp\clustalx.exe", FileView]) def rClick_ClustalX_aln(e): FileView=os.path.splitext(seq_inuse_entry.get())[0]+'.aln' subprocess.run(["ExtApp\clustalx.exe", FileView]) e.widget.focus() nclst=[ ('Cut' , lambda e=e: rClick_Cut(e)), ('Copy' , lambda e=e: rClick_Copy(e)), ('Paste', lambda e=e: rClick_Paste(e)), ('Select All', lambda e=e: rClick_Select_All(e)), ('Clear All', lambda e=e: rClick_Clear_All(e)), ('Copy to Clipboard', lambda e=e: rClick_Clipboard(e)), ('-', lambda e=e: rClick_Clipboard(e)), ('Seq with AliView', lambda e=e: rClick_AliView_seq(e)), ('Aln with AliView', lambda e=e: rClick_AliView_aln(e)), ('-', lambda e=e: rClick_Clipboard(e)), ('Seq with ClustalX', lambda e=e: rClick_ClustalX_seq(e)), ('Aln with ClustalX', lambda e=e: rClick_ClustalX_aln(e)), ] rmenu = tk.Menu(None, tearoff=0, takefocus=0) for (txt, cmd) in nclst: rmenu.add_command(label=txt, command=cmd) rmenu.tk_popup(e.x_root+40, e.y_root+10,entry="0") except tk.TclError: print (' - rClick menu, something wrong') pass return "break" def Load_Seq(): filepath = askopenfilename(filetypes=[("SEQ Files", "*.fasta;*.fas;*.gb;*.gbk;*.genbank"), ("All Files", "*.*")]) if not filepath: return f = open(filepath, 'r') f2 = f.read() seq_edit.delete('1.0', 'end') seq_edit.insert('1.0', f2) seq_inuse_entry.delete(0, tk.END) seq_inuse_entry.insert(0, (filepath)) f.close() seq_format=os.path.splitext(filepath)[1] print(seq_format) if ( seq_format in ['.gbk','.gb'] ) : format_seq='genbank' elif (seq_format in ['.fasta','.fas','.fa']): format_seq='fasta' elif (seq_format in ['.nexus','.nex','.ne']): format_seq='nexus' else: print('Format not defined ...') label_var.set(format_seq) def Save_Seq(): filepath = asksaveasfilename( defaultextension="",initialfile ="seq000.fasta", filetypes=[("Seq Files", "*.fasta;*.gb;*.genbank"), ("All Files", "*.*")], ) if not filepath: return f = open(filepath, 'w') f.write(seq_edit.get(1.0, tk.END)) f.close def Convert_Seq(): seq_file=seq_inuse_entry.get() format_seq=label_var.get() format_dest=Convert_Combo.get() conv_edit.delete('1.0', 'end') try: if (format_dest=='Fasta'): conv_file=aln_file=os.path.splitext(seq_file)[0]+'.fasta' count = SeqIO.convert(seq_file, format_seq, conv_file, "fasta") elif (format_dest=='Fasta2'): conv_file=aln_file=os.path.splitext(seq_file)[0]+'.fasta2' count = SeqIO.convert(seq_file, format_seq, conv_file, "fasta-2line") elif (format_dest=='Fastq'): conv_file=aln_file=os.path.splitext(seq_file)[0]+'.fastq' count = SeqIO.convert(seq_file, format_seq, conv_file, "fastq") elif (format_dest=='Fastq Sanger'): conv_file=aln_file=os.path.splitext(seq_file)[0]+'.fastq' count = SeqIO.convert(seq_file, format_seq, conv_file, "fastq-sanger") elif (format_dest=='Genbank'): conv_file=aln_file=os.path.splitext(seq_file)[0]+'.gb' count = SeqIO.convert(seq_file, format_seq, conv_file, "genbank") elif (format_dest=='embl'): conv_file=aln_file=os.path.splitext(seq_file)[0]+'.embl' count = SeqIO.convert(seq_file, format_seq, conv_file, "embl") elif (format_dest=='Nexus'): conv_file=aln_file=os.path.splitext(seq_file)[0]+'.nexus' count = SeqIO.convert(seq_file, format_seq, conv_file, "nexus") elif (format_dest=='tab'): conv_file=aln_file=os.path.splitext(seq_file)[0]+'.tab' count = SeqIO.convert(seq_file, format_seq, conv_file, "tab") else: messagebox.showwarning(title="Format Conversion", message='Method not defined ...' ) except ValueError as v_e: messagebox.showwarning(title="Format Conversion", message='Error executing aligment !' + str(v_e)) return False f = open(conv_file, 'r') f2 = f.read() conv_edit.insert('1.0', f2) messagebox.showwarning(title="Format Conversion", message=' Converted ' + str(count) + ' records' ) def Align_Seq(): seq_file=seq_inuse_entry.get() aln_file=os.path.splitext(seq_inuse_entry.get())[0]+'.aln' aln0_file=os.path.splitext(seq_inuse_entry.get())[0] aln1_file=os.path.splitext(seq_inuse_entry.get())[0]+'.best.nex' tre_file=os.path.splitext(seq_inuse_entry.get())[0]+'.dnd' aln_edit.delete('1.0', 'end') dnd_edit.delete('1.0', 'end') label0_var.set(' Align in process ...') window.update_idletasks() if (Align_Combo.get()=='Clustalw'): try: clustalw_exe = r"clustalw2.exe" clustalw_cline = ClustalwCommandline(clustalw_exe, infile=seq_file,type=SeqType_Combo.get()) print (clustalw_cline) assert os.path.isfile(clustalw_exe), "Clustal W executable missing" stdout, stderr = clustalw_cline() f = open(aln_file, 'r') f2 = f.read() aln_edit.insert('1.0', f2) tree = Phylo.read(tre_file, "newick") temp_out = StringIO() sys.stdout = temp_out Phylo.draw_ascii(tree) dnd_edit.insert('1.0', temp_out.getvalue()) sys.stdout = sys.__stdout__ Phylo.draw(tree, branch_labels=lambda c: c.branch_length) label0_var.set('') window.update_idletasks() except : messagebox.showwarning(title="Clustalw2", message='Error executing aligment !' ) label0_var.set('') window.update_idletasks() return False elif (Align_Combo.get()=='ClustalO'): try: clustalo_exe = r"clustalo.exe" clustalo_cline = ClustalOmegaCommandline(clustalo_exe, infile=seq_file, outfile=aln_file, force=True, outfmt='clu') print (clustalo_cline) assert os.path.isfile(clustalo_exe), "Clustal O executable missing" stdout, stderr = clustalo_cline() f = open(aln_file, 'r') f2 = f.read() aln_edit.insert('1.0', f2) label0_var.set('') window.update_idletasks() except : messagebox.showwarning(title="ClustalO", message='Error executing aligment !' ) label0_var.set('') window.update_idletasks() return False elif (Align_Combo.get()=='Prank'): try: prank_exe = r"prank.exe" prank_cline = PrankCommandline(d=seq_file, o=aln0_file, f=17, F=False, showtree=True) print (prank_cline) assert os.path.isfile(prank_exe), "Prank executable missing" stdout, stderr = prank_cline() finally : print(aln1_file) f = open(aln1_file, 'r') f2 = f.read() aln_edit.insert('1.0', f2) label0_var.set('') window.update_idletasks() return False elif (Align_Combo.get()=='Muscle'): try: muscle_exe = r"muscle.exe" muscle_cline = MuscleCommandline(input=seq_file, out=aln_file, clw=True, tree2=tre_file ) print (muscle_cline) assert os.path.isfile(muscle_exe), "Muscle executable missing" stdout, stderr = muscle_cline() f = open(aln_file, 'r') f2 = f.read() aln_edit.insert('1.0', f2) tree = Phylo.read(tre_file, "newick") temp_out = StringIO() sys.stdout = temp_out Phylo.draw_ascii(tree) dnd_edit.insert('1.0', temp_out.getvalue()) sys.stdout = sys.__stdout__ Phylo.draw(tree, branch_labels=lambda c: c.branch_length) label0_var.set('') window.update_idletasks() except : messagebox.showwarning(title="Muscle", message='Error executing aligment !' ) label0_var.set('') window.update_idletasks() return False elif (Align_Combo.get()=='Dialign'): try: dialign_exe = r"dialign-tx.exe" dialign_cline = DialignCommandline(input=seq_file, fn=aln_file, fa=True) assert os.path.isfile(dialign_exe), "Dialign executable missing" stdout, stderr = dialign_cline() f = open(aln_file, 'r') f2 = f.read() aln_edit.insert('1.0', f2) except : messagebox.showwarning(title="Dialign", message='Error executing aligment !' ) label0_var.set('') window.update_idletasks() return False elif (Align_Combo.get()=='Probcons'): probcons_exe = r"probcons.exe" probcons_cline = ProbconsCommandline(input=seq_file, clustalw=True) print (probcons_cline) assert os.path.isfile(probcons_exe), "Probcons executable missing" stdout, stderr = probcons_cline() with open(aln_file, "w") as handle: handle.write(stdout) f = open(aln_file, 'r') f2 = f.read() aln_edit.insert('1.0', f2) else: messagebox.showwarning(title="Align", message='Method not defined ...' ) label0_var.set('') window.update_idletasks() def Entrez_Search(): entrez_edit.delete('1.0', 'end') handle = Entrez.efetch(db=db_entry.get(), id=id_entry.get() , rettype=type_entry.get(), retmode=mode_entry.get()) entrez_edit.insert('1.0',handle.read()) def Swiss_Search(): try: swiss_edit.delete('1.0', 'end') handle = ExPASy.get_sprot_raw(accessions_entry.get()) swiss_edit.insert('1.0',handle.read()) except ValueError: messagebox.showwarning(title="ExPASy", message='Not found ...' ) def Swiss0_Search(): try: swiss_edit.delete('1.0', 'end') handle = ExPASy.get_prosite_raw(prosite_entry.get()) swiss_edit.insert('1.0',handle.read()) except ValueError: messagebox.showwarning(title="Prosite", message='Not found ...' ) def Swiss1_Search(): try: swiss_edit.delete('1.0', 'end') handle = ScanProsite.scan(seq=prosite1_entry.get()) swiss_edit.insert('1.0',handle.read()) except ValueError: messagebox.showwarning(title="Prosite", message='Not found ...' ) def Web(N): if (N=="0"): url = 'http://blast.ncbi.nlm.nih.gov/Blast.cgi' elif (N=="1"): url = 'http://www.ebi.ac.uk/Tools/msa/tcoffee/' elif (N=="2"): url = 'http://www.ebi.ac.uk/Tools/msa/mafft/' elif (N=="3"): url = 'http://www.ebi.ac.uk/goldman-srv/webprank/' elif (N=="4"): url = 'http://toolkit.tuebingen.mpg.de/probcons' elif (N=="5"): url = 'http://rna.informatik.uni-freiburg.de/LocARNA/Input.jsp' elif (N=="6"): url = 'http://rna.informatik.uni-freiburg.de/CARNA/Input.jsp' elif (N=="7"): url = 'http://rnacentral.org/' elif (N=="8"): url = 'http://www.phylogeny.fr/one_task.cgi?task_type=phyml/' elif (N=="9"): url = 'http://www.phylogeny.fr/one_task.cgi?task_type=tnt' elif (N=="10"): url = 'http://www.phylogeny.fr/one_task.cgi?task_type=bionj' elif (N=="11"): url = 'http://www.phylogeny.fr/one_task.cgi?task_type=mrbayes' elif (N=="12"): url = 'http://iubio.bio.indiana.edu/treeapp/treeprint-form.html' elif (N=="13"): url = 'http://primer3plus.com/cgi-bin/dev/primer3plus.cgi' elif (N=="14"): url = 'http://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi' elif (N=="15"): url = 'http://genome.ucsc.edu/cgi-bin/hgPcr' elif (N=="16"): url = 'http://mobyle.pasteur.fr/cgi-bin/portal.py#welcome' elif (N=="17"): url = 'https://usegalaxy.org/' elif (N=="18"): url = 'http://emboss.bioinformatics.nl/' elif (N=="19"): url = 'http://www.bioinformatics.org/sewer/' elif (N=="20"): url = 'http://www.bioservers.org/bioserver/' elif (N=="21"): url = 'http://www.trex.uqam.ca/index.php?action=home&tools=trex' elif (N=="22"): url = 'http://www.expasy.org/' elif (N=="23"): url = 'http://toolkit.lmb.uni-muenchen.de/' elif (N=="24"): url = 'http://www.lansys-sistemas.com/biolansys/sms2/' webbrowser.register('firefox',None,webbrowser.BackgroundBrowser(PATH_FIREFOX)) webbrowser.get('firefox').open(url) def ExtApp(N): if (N=="0"): subprocess.run(["ExtApp\Clustalx.exe", ""]) elif (N=="1"): subprocess.run(["ExtApp\Aliview.exe", ""]) elif (N=="2"): subprocess.run(["ExtApp\FigTree.exe", ""]) # GUI window = ThemedTk(theme='scidblue') window.title("BioPython GUI") center_window(1040,640) style = ttk.Style(window) # Notebook style s = ttk.Style() s.configure('TNotebook.Tab', font=('Times','10' ) ) label_var = tk.StringVar() label0_var = tk.StringVar() # Main Frame main_frame = ttk.Frame(window) main_frame.pack(fill='both', expand=True) # End Main Frame # Top Frame top_frame = tk.Frame(main_frame, bd=0, relief=tk.SOLID, padx=0, pady=0) top_frame.pack(side=tk.TOP, fill=tk.X) LoadSeq_btn = tk.Button(top_frame, width=8, height=1 ,text=' Load Seq ', font=('Lucida', 9,'bold'), command=Load_Seq) CrearToolTip(LoadSeq_btn," Open Sequence File ") LoadSeq_btn.grid(row=0, column=0, pady=3, padx=(2,2) ) SaveSeq_btn = tk.Button(top_frame, width=8, height=1 ,text=' Save Seq ', font=('Lucida', 9,'bold'), command=Save_Seq) CrearToolTip(SaveSeq_btn," Save Sequence File ") SaveSeq_btn.grid(row=0, column=1, pady=3, padx=(0,2) ) Align_Combo = ttk.Combobox(top_frame, state="readonly",width=8,font=('Lucida', 9,'bold') ) CrearToolTip(Align_Combo," Align Method ") Align_Combo.set('Clustalw') Align_Combo_Values=['Clustalw','ClustalO','Muscle','Prank','Probcons'] Align_Combo['values'] = Align_Combo_Values Align_Combo.grid(sticky="W",row=0, column=2, padx=(10,3), pady=(2,2)) AlignSeq_btn = tk.Button(top_frame, width=8, height=1 ,text=' Align ', font=('Lucida', 9,'bold'), command=Align_Seq) CrearToolTip(AlignSeq_btn," Align Seq ") AlignSeq_btn.grid(row=0, column=3, pady=3, padx=(0,5) ) Convert_Combo = ttk.Combobox(top_frame, state="readonly",width=12,font=('Lucida', 9,'bold') ) CrearToolTip(Convert_Combo," Convert Format ") Convert_Combo.set('Fasta') Convert_Combo_Values=['Fasta','Fasta2','Fastq','Fastq Sanger','Nexus','Genbank','embl','tab'] Convert_Combo['values'] = Convert_Combo_Values Convert_Combo.grid(sticky="W",row=0, column=4, padx=(10,3), pady=(2,2)) Convert_btn = tk.Button(top_frame, width=10, height=1 ,text=' Conversion ', font=('Lucida', 9,'bold'), command=Convert_Seq) CrearToolTip(Convert_btn," Convert Seq ") Convert_btn.grid(row=0, column=5, pady=3, padx=(0,5) ) process_label = tk.Label(top_frame, text="", textvariable=label0_var, bd=1, anchor=tk.W, width=20,height=1,font=('Lucida', 9,'bold'),foreground = "red") process_label.grid(row=0, column=6, pady=3, padx=(10,2) ) # End Top Frame # Bottom Frame bottom_frame = tk.Frame(main_frame,padx=0, pady=0) bottom_frame.pack(side=tk.BOTTOM, fill=tk.X) seq_inuse_label = tk.Label(bottom_frame,width=8,text="Seq File:",font=('Lucida', 9,'bold'),anchor=tk.W) seq_inuse_label.grid(row=0, column=0, pady=3, padx=(10,2) ) seq_inuse_entry = ttk.Entry(bottom_frame,width=55,font=('Lucida', 9,'bold')) ; seq_inuse_entry.insert(0, "") seq_inuse_entry.grid(row=0, column=1, pady=3, padx=(2,2) ) format_label = tk.Label(bottom_frame, text="", textvariable=label_var, bd=1, relief=tk.SUNKEN, anchor=tk.W, width=10,height=1,font=('Lucida', 9,'bold'), background = "#7F8F9A",foreground = "white") format_label.grid(row=0, column=2, pady=3, padx=(10,2) ) SeqType_Combo = ttk.Combobox(bottom_frame, state="readonly",width=8,font=('Lucida', 9,'bold') ) CrearToolTip(SeqType_Combo," Sequence Type ") SeqType_Combo.set('DNA') SeqType_Combo_Values=['DNA','PROTEIN'] SeqType_Combo['values'] = SeqType_Combo_Values SeqType_Combo.grid(sticky="W",row=0, column=3, padx=(10,3), pady=(2,2)) # End Bottom Frame # Center Frame Center_frame = tk.Frame(main_frame,width=180,bd=0, relief=tk.SOLID, padx=0, pady=0) Center_frame.pack(side=tk.LEFT,fill="both", expand=1) # Notebook notebook0 = ttk.Notebook(Center_frame) notebook0.pack(padx=0,pady=0, expand = 1, fill ="both") # create tabs frame01 = ttk.Frame(notebook0) ; frame01.pack(fill='both', expand=True) frame02 = ttk.Frame(notebook0) ; frame02.pack(fill='both', expand=True) frame03 = ttk.Frame(notebook0) ; frame03.pack(fill='both', expand=True) frame04 = ttk.Frame(notebook0) ; frame04.pack(fill='both', expand=True) frame05 = ttk.Frame(notebook0) ; frame05.pack(fill='both', expand=True) frame06 = ttk.Frame(notebook0) ; frame06.pack(fill='both', expand=True) # add tabs to notebook notebook0.add(frame01, text=' Sequence ') notebook0.add(frame02, text=' Align ') notebook0.add(frame03, text=' Phylo Tree ') notebook0.add(frame04, text=' Conversion ') notebook0.add(frame05, text=' Entrez ') notebook0.add(frame06, text=' SwissProt ') # First tab seq_edit = scrolledtext.ScrolledText(frame01,font=('Lucida console', 10), height=45, background = "#243642",foreground = "white",insertbackground="red") seq_edit.bind('<Button-3>',rClicker, add='') seq_edit.pack(side=tk.TOP,fill=tk.X,expand=True) # Second tab aln_edit = scrolledtext.ScrolledText(frame02,font=('Lucida console', 10), height=45, background = "#243642",foreground = "white",insertbackground="red") aln_edit.bind('<Button-3>',rClicker, add='') aln_edit.pack(side=tk.TOP,fill=tk.X,expand=True) # Third tab dnd_edit = scrolledtext.ScrolledText(frame03,font=('Lucida console', 10), height=45, background = "#243642",foreground = "white",insertbackground="red") dnd_edit.bind('<Button-3>',rClicker, add='') dnd_edit.pack(side=tk.TOP,fill=tk.X,expand=True) # Fourth tab conv_edit = scrolledtext.ScrolledText(frame04,font=('Lucida console', 10), height=45, background = "#243642",foreground = "white",insertbackground="red") conv_edit.bind('<Button-3>',rClicker, add='') conv_edit.pack(side=tk.TOP,fill=tk.X,expand=True) # Five tab entrez_top_frame = tk.Frame(frame05,padx=0, pady=0) entrez_top_frame.pack(side=tk.TOP, fill=tk.X) db_label = tk.Label(entrez_top_frame,width=8,text="Entrez:",font=('Lucida', 9,'bold'),anchor=tk.W) db_label.grid(row=0, column=0, pady=3, padx=(10,2) ) db_entry = ttk.Entry(entrez_top_frame,width=10,font=('Lucida', 9,'bold')) ; db_entry.insert(0, "nucleotide") db_entry.grid(row=0, column=1, pady=3, padx=(2,2) ) id_entry = ttk.Entry(entrez_top_frame,width=30,font=('Lucida', 9,'bold')) ; id_entry.insert(0, "6273291,6273290,6273289") id_entry.grid(row=0, column=2, pady=3, padx=(2,2) ) type_entry = ttk.Entry(entrez_top_frame,width=10,font=('Lucida', 9,'bold')) ; type_entry.insert(0, "gb") type_entry.grid(row=0, column=3, pady=3, padx=(2,2) ) mode_entry = ttk.Entry(entrez_top_frame,width=10,font=('Lucida', 9,'bold')) ; mode_entry.insert(0, "text") mode_entry.grid(row=0, column=4, pady=3, padx=(2,2) ) entrez_btn = tk.Button(entrez_top_frame, width=8, height=1 ,text=' Search ', font=('Lucida', 9,'bold'), command=Entrez_Search) CrearToolTip(entrez_btn," Open Sequence File ") entrez_btn.grid(row=0, column=5, pady=3, padx=(2,2) ) entrez_edit = scrolledtext.ScrolledText(frame05,font=('Lucida console', 10), height=45, background = "#243642",foreground = "white",insertbackground="red") entrez_edit.bind('<Button-3>',rClicker, add='') entrez_edit.pack(side=tk.TOP,fill=tk.X,expand=True) # Six tab swiss_top_frame = tk.Frame(frame06,padx=0, pady=0) swiss_top_frame.pack(side=tk.TOP, fill=tk.X) swiss_top_frame0 = tk.Frame(frame06,padx=0, pady=0) swiss_top_frame0.pack(side=tk.TOP, fill=tk.X) swiss_label = tk.Label(swiss_top_frame,width=14,text="Accession/Name:",font=('Lucida', 9,'bold'),anchor=tk.W) swiss_label.grid(row=0, column=0, pady=3, padx=(10,2) ) accessions_entry = ttk.Entry(swiss_top_frame,width=15,font=('Lucida', 9,'bold')) ; accessions_entry.insert(0, "O23729") accessions_entry.grid(row=0, column=1, pady=3, padx=(2,2) ) swiss_btn = tk.Button(swiss_top_frame, width=8, height=1 ,text=' Search ', font=('Lucida', 9,'bold'), command=Swiss_Search) CrearToolTip(swiss_btn," Search SwissProt ") swiss_btn.grid(row=0, column=5, pady=3, padx=(2,2) ) swiss0_label = tk.Label(swiss_top_frame,width=6,text=" Prosite:",font=('Lucida', 9,'bold'),anchor=tk.W) swiss0_label.grid(row=0, column=6, pady=3, padx=(10,2) ) prosite_entry = ttk.Entry(swiss_top_frame,width=15,font=('Lucida', 9,'bold')) ; prosite_entry.insert(0, "PS50240") prosite_entry.grid(row=0, column=7, pady=3, padx=(2,2) ) swiss0_btn = tk.Button(swiss_top_frame, width=8, height=1 ,text=' Search ', font=('Lucida', 9,'bold'), command=Swiss0_Search) CrearToolTip(swiss0_btn," Search Prosite ") swiss0_btn.grid(row=0, column=8, pady=3, padx=(2,2) ) swiss1_label = tk.Label(swiss_top_frame0,width=8,text="Sequence:",font=('Lucida', 9,'bold'),anchor=tk.W) swiss1_label.grid(row=1, column=0, pady=3, padx=(10,2) ) prosite1_entry = ttk.Entry(swiss_top_frame0,width=105,font=('Lucida', 9,'bold')) ; prosite1_entry.insert(0, "MGSKRGISSRHHSLSSYEIMFAALFAILVVLCAGLIAVSCLTIKESQRGAALGQSHEARATFKITSGVTYNPNLQDKLSV") prosite1_entry.grid(row=1, column=1, pady=3, padx=(2,2) ) swiss1_btn = tk.Button(swiss_top_frame0, width=8, height=1 ,text=' Search ', font=('Lucida', 9,'bold'), command=Swiss1_Search) CrearToolTip(swiss1_btn," Search Prosite ") swiss1_btn.grid(row=1, column=2, pady=3, padx=(2,2) ) swiss_edit = scrolledtext.ScrolledText(frame06,font=('Lucida console', 10), height=45, background = "#243642",foreground = "white",insertbackground="red") swiss_edit.bind('<Button-3>',rClicker, add='') swiss_edit.pack(side=tk.TOP,fill=tk.X,expand=True) # End Center Frame # Menu bar menubar = tk.Menu(window) filemenu = tk.Menu(menubar, tearoff=0) filemenu.add_command(label="Exit" , command=Close) menubar.add_cascade(label="File" , menu=filemenu) alignmenu = tk.Menu(menubar, tearoff=0) alignmenu.add_command(label="Blast at NCBI", command=lambda: Web("0")) alignmenu.add_command(label="T-Coffee at EMBL-EBI", command=lambda: Web("1")) alignmenu.add_command(label="MAFFT at EMBL-EBI", command=lambda: Web("2")) alignmenu.add_command(label="webPRANK at EMBL-EBI", command=lambda: Web("3")) alignmenu.add_command(label="ProbCons at MPlank Soc.", command=lambda: Web("4")) menubar.add_cascade(label="Web Align", menu=alignmenu) rnamenu = tk.Menu(menubar, tearoff=0) rnamenu.add_command(label="LocARNA", command=lambda: Web("5")) rnamenu.add_command(label="CARNA", command=lambda: Web("6")) rnamenu.add_command(label="RNAcentral", command=lambda: Web("7")) menubar.add_cascade(label="Web RNA", menu=rnamenu) phylomenu = tk.Menu(menubar, tearoff=0) phylomenu.add_command(label="PhyML", command=lambda: Web("8")) phylomenu.add_command(label="TNT", command=lambda: Web("9")) phylomenu.add_command(label="BioNJ", command=lambda: Web("10")) phylomenu.add_command(label="MrBayes", command=lambda: Web("11")) phylomenu.add_command(label="Phylodendron", command=lambda: Web("12")) menubar.add_cascade(label="Web Phylo", menu=phylomenu) primermenu = tk.Menu(menubar, tearoff=0) primermenu.add_command(label="PrimerPlus", command=lambda: Web("13")) primermenu.add_command(label="Primer-BLAST", command=lambda: Web("14")) primermenu.add_command(label="In-Silico PCR", command=lambda: Web("15")) menubar.add_cascade(label="Web Primer", menu=primermenu) suitesmenu = tk.Menu(menubar, tearoff=0) suitesmenu.add_command(label="Mobyle", command=lambda: Web("16")) suitesmenu.add_command(label="Galaxy", command=lambda: Web("17")) suitesmenu.add_command(label="EMBOSS", command=lambda: Web("18")) suitesmenu.add_command(label="SeWeR", command=lambda: Web("19")) suitesmenu.add_command(label="BioServers", command=lambda: Web("20")) suitesmenu.add_command(label="T-REX", command=lambda: Web("21")) suitesmenu.add_command(label="ExPASy", command=lambda: Web("22")) suitesmenu.add_command(label="Bio/Toolkit", command=lambda: Web("23")) suitesmenu.add_command(label="SMS2", command=lambda: Web("24")) menubar.add_cascade(label="Web Suites", menu=suitesmenu) extpmenu = tk.Menu(menubar, tearoff=0) extpmenu.add_command(label="Clustalx", command=lambda: ExtApp("0")) extpmenu.add_command(label="AliView", command=lambda: ExtApp("1")) extpmenu.add_command(label="FigTree", command=lambda: ExtApp("2")) menubar.add_cascade(label="Ext Apps", menu=extpmenu) helpmenu = tk.Menu(menubar, tearoff=0) helpmenu.add_command(label="About...", command=About) menubar.add_cascade(label="Help" , menu=helpmenu) window.config(menu=menubar) # End Menu Bar #window.state('zoomed') window.mainloop()  

Debe crearse una subcarpeta llamada ExtApp que contenga las aplicacione externas: ClustalX, AliView, FigTree. Adicionalmente, en la misma ubicación del script, deben copiarse las aplicaciones de alineación de secuencias: Clustalw, ClustalO, Muscle, Prank, Probcoms.