def Itol_Tree_m_sd3(pfamid, datapath, outpath):#{{{
"""Phylogenetic tree with species definition
the Kindom use branch colordefinition, and others using color strips
"""
tree = datapath + os.sep + pfamid + '.tree'
t = Tree(tree)
leaves = t.get_leaves()
lst_leaves_name = []
for leaf in leaves:
lst_leaves_name.append(leaf.name)
numLeave = len(lst_leaves_name)
leaves_name_set = set(lst_leaves_name)
# read species definition
speciesfile = "%s/%s.species"%(datapath, pfamid)
speciesDict = myfunc.Read_species_sd(speciesfile)
# create branch color definition file for kingdom
lst_kingdom = ["Archaea","Bacteria", "Eukaryota" ]
lst_color_kingdom = ["#ff0000", "#0066ff","#cc6600"]
species_colordef_file = "%s/%s.kingdom.colordef.txt"%(outpath, pfamid)
color_dict_kingdom = {}
this_speciesDict = {}
for seqid in speciesDict:
speciesname = speciesDict[seqid][0]
this_speciesDict[seqid] = speciesname
for i in range(len(lst_kingdom)):
idd = lst_kingdom[i]
color_dict_kingdom[idd] = lst_color_kingdom[i]
myfunc.WriteKingdomColorDefFile(species_colordef_file, this_speciesDict, leaves_name_set, color_dict_kingdom)
# generate the next three levels of classification
for level in [1,2,3]:
outfile = "%s/%s.species.level_%d.txt"%(outpath, pfamid, level)
this_speciesDict = {}
speciesIDSet = set([])
for seqid in speciesDict:
try:
speciesname = speciesDict[seqid][level]
speciesIDSet.add(speciesname)
this_speciesDict[seqid] = speciesname
except IndexError as KeyError:
pass
color_dict = {}
lst_color = list(blue.range_to(red,len(speciesIDSet)))
lst_speciesID = list(speciesIDSet)
for i in range(len(lst_speciesID)):
idd = lst_speciesID[i]
color_dict[idd] = lst_color[i].get_hex_l()
myfunc.WriteSpeciesColorStripDefFile(outfile, this_speciesDict, leaves_name_set, color_dict)
#Create the Itol class
itl = Itol()
#Set the tree file
(datafile1, datafile2, datafile3, datafile4) = ("", "", "", "")
if not os.path.exists(tree):
print("tree file %s does not exist. Ignore" %(tree), file=sys.stderr)
return 1
fontsize = GetFontSize(numLeave)
datafile1 = "%s/%s.species.level_%d.txt"%(outpath, pfamid, 1)
datafile2 = "%s/%s.species.level_%d.txt"%(outpath, pfamid, 2)
datafile3 = "%s/%s.species.level_%d.txt"%(outpath, pfamid, 3)
colordeffile = species_colordef_file
if os.path.exists(colordeffile):
itl.add_variable('colorDefinitionFile', colordeffile)
itl.add_variable('colorDefinitionLabel', "Kingdom")
#===================================
itl.add_variable('treeFile',tree)
itl.add_variable('treeName','SD3')
itl.add_variable('treeFormat','newick')
#===================================
if os.path.exists(datafile1):
itl.add_variable('datafile1File',datafile1)
itl.add_variable('datafile1Label','Phylum')
itl.add_variable('datafile1Separator','comma')
itl.add_variable('datafile1Type','colorstrip')
itl.add_variable('datafile1StripWidth','100')
itl.add_variable('datafile1ColoringType','both')
itl.add_variable('datafile1PreventOverlap','1')
#===================================
if os.path.exists(datafile2):
itl.add_variable('datafile2File',datafile2)
itl.add_variable('datafile2Label','Class')
itl.add_variable('datafile2Separator','comma')
itl.add_variable('datafile2Type','colorstrip')
itl.add_variable('datafile2StripWidth','100')
itl.add_variable('datafile2ColoringType','both')
itl.add_variable('datafile2PreventOverlap','1')
#===================================
if os.path.exists(datafile3):
itl.add_variable('datafile3File',datafile3)
itl.add_variable('datafile3Label','Order')
itl.add_variable('datafile3Separator','comma')
itl.add_variable('datafile3Type','colorstrip')
itl.add_variable('datafile3StripWidth','100')
itl.add_variable('datafile3ColoringType','both')
itl.add_variable('datafile3PreventOverlap','1')
#===================================
# Check parameters
# itl.print_variables()
#Submit the tree
print('')
print('Uploading the tree. This may take some time depending on how large the tree is and how much load there is on the itol server')
good_upload = itl.upload()
if good_upload == False:
print('There was an error:'+itl.comm.upload_output)
sys.exit(1)
#Read the tree ID
print('Tree ID: '+str(itl.comm.tree_id))
#Read the iTOL API return statement
print('iTOL output: '+str(itl.comm.upload_output))
#Website to be redirected to iTOL tree
print('Tree Web Page URL: '+itl.get_webpage())
# Warnings associated with the upload
print('Warnings: '+str(itl.comm.warnings))
#Export to pdf
itol_exporter = itl.get_itol_export()
#itol_exporter = itolexport.ItolExport()
#itol_exporter.set_export_param_value('tree','18793532031912684633930')
itol_exporter.set_export_param_value('format', 'eps')
itol_exporter.set_export_param_value('display_mode',"2")
itol_exporter.set_export_param_value('current_font_size',fontsize)
itol_exporter.set_export_param_value('align_labels',"1")
itol_exporter.set_export_param_value('datafileList','dataset1')
extname = "-itol-sd3"
epsfile = outpath + os.sep + pfamid + extname + '.eps'
pdffile = outpath + os.sep + pfamid + extname + '.pdf'
jpgfile = outpath + os.sep + pfamid + extname + '.jpg'
pngfile = outpath + os.sep + pfamid + extname + '.png'
thumbfile = outpath + os.sep + "thumb." + pfamid + extname + '.jpg'
itol_exporter.export(epsfile)
os.system("epstopdf %s" % epsfile )
os.system("convert %s %s" % (epsfile, jpgfile) )
os.system("convert -thumbnail 200 %s %s" % (jpgfile, thumbfile))
print('exported tree to ',pdffile)
def Itol_Tree_m_sd1(pfamid, datapath, outpath):#{{{
"""Phylogenetic tree with numTM_io and subfamilies branch coloring
"""
tree = datapath + os.sep + pfamid + '.tree'
t = Tree(tree)
leaves = t.get_leaves()
lst_leaves_name = []
for leaf in leaves:
lst_leaves_name.append(leaf.name)
numLeave = len(lst_leaves_name)
# read subfamily definition
subfamfile = "%s/%s.subfamilies"%(datapath, pfamid)
subfam_idlist = []
subfamDict = myfunc.Read_subfamily(subfamfile, subfam_idlist)
numSubFam = len(subfam_idlist)
# create subfamily branch color definition file
subfam_colordef_file = "%s/%s.subfamilies.colordef.txt"%(outpath, pfamid)
lst_color = list(blue.range_to(red,numSubFam))
color_dict = {}
for i in range(numSubFam):
famid = subfam_idlist[i]
color = lst_color[i].get_hex_l()
color_dict[famid] = lst_color[i].get_hex_l()
myfunc.WriteSubFamColorDef(subfam_colordef_file, subfamDict, lst_leaves_name, color_dict)
#Create the Itol class
itl = Itol()
#Set the tree file
(datafile1, datafile2, datafile3, datafile4) = ("", "", "", "")
if not os.path.exists(tree):
print("tree file %s does not exist. Ignore" %(tree), file=sys.stderr)
return 1
fontsize = GetFontSize(numLeave)
datafile1 = datapath + os.sep + pfamid + '.numTM_and_io.txt'
colordeffile = subfam_colordef_file
if os.path.exists(colordeffile):
itl.add_variable('colorDefinitionFile', colordeffile)
itl.add_variable('colorDefinitionLabel', "Subfamilies")
#===================================
itl.add_variable('treeFile',tree)
itl.add_variable('treeName','SD1')
itl.add_variable('treeFormat','newick')
#===================================
if os.path.exists(datafile1):
itl.add_variable('datafile1File',datafile1)
itl.add_variable('datafile1Label','numTM_and_io')
itl.add_variable('datafile1Separator','comma')
itl.add_variable('datafile1Type','multibar')
itl.add_variable('datafile1PreventOverlap','1')
itl.add_variable('datafile1Color','#FF0000')
#===================================
# Check parameters
# itl.print_variables()
#Submit the tree
print('')
print('Uploading the tree. This may take some time depending on how large the tree is and how much load there is on the itol server')
good_upload = itl.upload()
if good_upload == False:
print('There was an error:'+itl.comm.upload_output)
sys.exit(1)
#Read the tree ID
print('Tree ID: '+str(itl.comm.tree_id))
#Read the iTOL API return statement
print('iTOL output: '+str(itl.comm.upload_output))
#Website to be redirected to iTOL tree
print('Tree Web Page URL: '+itl.get_webpage())
# Warnings associated with the upload
print('Warnings: '+str(itl.comm.warnings))
#Export to pdf
itol_exporter = itl.get_itol_export()
#itol_exporter = itolexport.ItolExport()
#itol_exporter.set_export_param_value('tree','18793532031912684633930')
itol_exporter.set_export_param_value('format', 'eps')
itol_exporter.set_export_param_value('display_mode',"2")
itol_exporter.set_export_param_value('current_font_size',fontsize)
itol_exporter.set_export_param_value('align_labels',"1")
itol_exporter.set_export_param_value('datafileList','dataset1')
extname = "-itol-sd1"
epsfile = outpath + os.sep + pfamid + extname + '.eps'
pdffile = outpath + os.sep + pfamid + extname + '.pdf'
jpgfile = outpath + os.sep + pfamid + extname + '.jpg'
pngfile = outpath + os.sep + pfamid + extname + '.png'
thumbfile = outpath + os.sep + "thumb." + pfamid + extname + '.jpg'
itol_exporter.export(epsfile)
os.system("epstopdf %s" % epsfile )
os.system("convert %s %s" % (epsfile, jpgfile) )
os.system("convert -thumbnail 200 %s %s" % (jpgfile, thumbfile))
print('exported tree to ',pdffile)
def Itol_Tree_m_sd2(pfamid, datapath, outpath):#{{{
tree = datapath + os.sep + pfamid + '.tree'
t = Tree(tree)
leaves = t.get_leaves()
lst_leaves_name = []
for leaf in leaves:
lst_leaves_name.append(leaf.name)
numLeave = len(lst_leaves_name)
leaves_name_set = set(lst_leaves_name)
# read seqlen file
seqlenfile = "%s/%s.seqlen.txt"%(datapath, pfamid)
seqlen_dict = myfunc.ReadSeqLengthDict(seqlenfile)
# read subfamily definition
domain_idlist = []
domainfile = "%s/%s.mdp"%(datapath, pfamid)
domain_dict = myfunc.Read_domain_sd(domainfile, domain_idlist)
domain_colordef_file = "%s/%s.mdp.colordef.txt"%(datapath, pfamid)
WriteDomainColorDefFile(domain_colordef_file, domain_dict, domain_idlist, seqlen_dict, leaves_name_set)
#Create the Itol class
itl = Itol()
#Set the tree file
(datafile1, datafile2, datafile3, datafile4) = ("", "", "", "")
if not os.path.exists(tree):
print("tree file %s does not exist. Ignore" %(tree), file=sys.stderr)
return 1
fontsize = GetFontSize(numLeave)
datafile1 = domain_colordef_file
# colordeffile = subfam_colordef_file
# if os.path.exists(colordeffile):
# itl.add_variable('colorDefinitionFile', colordeffile)
# itl.add_variable('colorDefinitionLabel', "Subfamilies")
#===================================
itl.add_variable('treeFile',tree)
itl.add_variable('treeName','SD2')
itl.add_variable('treeFormat','newick')
#===================================
if os.path.exists(datafile1):
itl.add_variable('datafile1File',datafile1)
itl.add_variable('datafile1Label','Domain architecture')
itl.add_variable('datafile1Separator','comma')
itl.add_variable('datafile1Type','domains')
itl.add_variable('datafile1ProtSizeMax','1000')
itl.add_variable('datafile1PreventOverlap','1')
itl.add_variable('datafile1CirclesSpacing','100')
#===================================
# Check parameters
# itl.print_variables()
#Submit the tree
print('')
print('Uploading the tree. This may take some time depending on how large the tree is and how much load there is on the itol server')
good_upload = itl.upload()
if good_upload == False:
print('There was an error:'+itl.comm.upload_output)
sys.exit(1)
#Read the tree ID
print('Tree ID: '+str(itl.comm.tree_id))
#Read the iTOL API return statement
print('iTOL output: '+str(itl.comm.upload_output))
#Website to be redirected to iTOL tree
print('Tree Web Page URL: '+itl.get_webpage())
# Warnings associated with the upload
print('Warnings: '+str(itl.comm.warnings))
#Export to pdf
itol_exporter = itl.get_itol_export()
#itol_exporter = itolexport.ItolExport()
#itol_exporter.set_export_param_value('tree','18793532031912684633930')
itol_exporter.set_export_param_value('format', 'eps')
itol_exporter.set_export_param_value('display_mode',"2")
itol_exporter.set_export_param_value('current_font_size',fontsize)
itol_exporter.set_export_param_value('align_labels',"1")
itol_exporter.set_export_param_value('datafileList','dataset1')
extname = "-itol-sd2"
epsfile = outpath + os.sep + pfamid + extname + '.eps'
pdffile = outpath + os.sep + pfamid + extname + '.pdf'
jpgfile = outpath + os.sep + pfamid + extname + '.jpg'
pngfile = outpath + os.sep + pfamid + extname + '.png'
thumbfile = outpath + os.sep + "thumb." + pfamid + extname + '.jpg'
itol_exporter.export(epsfile)
os.system("epstopdf %s" % epsfile )
os.system("convert %s %s" % (epsfile, jpgfile) )
os.system("convert -thumbnail 200 %s %s" % (jpgfile, thumbfile))
print('exported tree to ',pdffile)
def Itol_Tree_m1(pfamid, datapath, outpath):#{{{
# TM helices are treated as domains
#Create the Itol class
itl = Itol()
#Set the tree file
tree = datapath + os.sep + pfamid + '.tree'
(datafile1, datafile2, datafile3, datafile4) = ("", "", "", "")
if not os.path.exists(tree):
print("tree file %s does not exist. Ignore" %(tree), file=sys.stderr)
return 1
t = Tree(tree)
leaves = t.get_leaves()
numLeave = len(leaves)
fontsize = GetFontSize(numLeave)
datafile1 = datapath + os.sep + pfamid + '.numTM_and_io.txt'
datafile2 = datapath + os.sep + pfamid + '.cmpclass.colordef.txt'
# datafile3 = datapath + os.sep + pfamid + '.ntermstate.colordef.txt'
datafile4 = datapath + os.sep + pfamid + '.cluster.colordef.txt'
colordeffile = datapath + os.sep + pfamid + '.pfam.colordef.txt'
branchlabelfile = datapath + os.sep + pfamid + '.branchlabel.txt'
#===================================
itl.add_variable('treeFile',tree)
itl.add_variable('treeName','PF00854')
itl.add_variable('treeFormat','newick')
if os.path.exists(colordeffile):
itl.add_variable('colorDefinitionFile', colordeffile)
if os.path.exists(branchlabelfile):
itl.add_variable('branchLabelsFile', branchlabelfile)
#===================================
if os.path.exists(datafile1):
itl.add_variable('datafile1File',datafile1)
itl.add_variable('datafile1Label','numTM_and_io')
itl.add_variable('datafile1Separator','comma')
itl.add_variable('datafile1Type','multibar')
itl.add_variable('datafile1PreventOverlap','1')
itl.add_variable('datafile1Color','#FF0000')
#===================================
if os.path.exists(datafile2):
itl.add_variable('datafile2File', datafile2)
itl.add_variable('datafile2Label', 'cmpclass')
itl.add_variable('datafile2Separator','comma')
itl.add_variable('datafile2Type','colorstrip')
itl.add_variable('datafile2StripWidth','200')
itl.add_variable('datafile2PreventOverlap','1')
itl.add_variable('datafile2ColoringType','both')
#===================================
if os.path.exists(datafile3):
itl.add_variable('datafile3File', datafile3)
itl.add_variable('datafile3Label', 'NtermState')
itl.add_variable('datafile3Separator','comma')
itl.add_variable('datafile3Type','colorstrip')
itl.add_variable('datafile3StripWidth','200')
itl.add_variable('datafile3PreventOverlap','1')
itl.add_variable('datafile3ColoringType','both')
#===================================
if os.path.exists(datafile4):
itl.add_variable('datafile4File', datafile4)
itl.add_variable('datafile4Label', 'cluster')
itl.add_variable('datafile4Separator','comma')
itl.add_variable('datafile4Type','colorstrip')
itl.add_variable('datafile4StripWidth','200')
itl.add_variable('datafile4PreventOverlap','1')
itl.add_variable('datafile4ColoringType','both')
itl.add_variable('datafile4BranchColoringType','both')
#itl.add_variable('datafile1BarSizeMax','1')
#===================================
# Check parameters
# itl.print_variables()
#Submit the tree
print('')
print('Uploading the tree. This may take some time depending on how large the tree is and how much load there is on the itol server')
good_upload = itl.upload()
if good_upload == False:
print('There was an error:'+itl.comm.upload_output)
sys.exit(1)
#Read the tree ID
print('Tree ID: '+str(itl.comm.tree_id))
#Read the iTOL API return statement
print('iTOL output: '+str(itl.comm.upload_output))
#Website to be redirected to iTOL tree
print('Tree Web Page URL: '+itl.get_webpage())
# Warnings associated with the upload
print('Warnings: '+str(itl.comm.warnings))
#Export to pdf
print('Exporting to pdf')
itol_exporter = itl.get_itol_export()
#itol_exporter = itolexport.ItolExport()
#itol_exporter.set_export_param_value('tree','18793532031912684633930')
itol_exporter.set_export_param_value('format', 'eps')
itol_exporter.set_export_param_value('display_mode',"2")
itol_exporter.set_export_param_value('current_font_size',fontsize)
itol_exporter.set_export_param_value('align_labels',"1")
itol_exporter.set_export_param_value('datafileList','dataset1')
epsfile = outpath + os.sep + pfamid + '-itol.eps'
pdffile = outpath + os.sep + pfamid + '-itol.pdf'
jpgfile = outpath + os.sep + pfamid + '-itol.jpg'
thumbfile = outpath + os.sep + "thumb." + pfamid + '-itol.jpg'
itol_exporter.export(epsfile)
os.system("epstopdf %s" % epsfile )
os.system("convert %s %s" % (epsfile, jpgfile) )
os.system("convert -thumbnail 200 %s %s" % (jpgfile, thumbfile))
print('exported tree to ',pdffile)