def GetTreeListOrder(treefile, outpath):
#Create the Itol class
itl = Itol()
#Set the tree file
tree = treefile
dirname = os.path.dirname(treefile)
if dirname == "":
dirname = "."
if outpath == "":
outpath = dirname
elif not os.path.exists(outpath):
os.system("mkdir -p %s" % (outpath))
rootname = os.path.basename(os.path.splitext(treefile)[0])
#===================================
itl.add_file(tree)
itl.params['treeName'] = rootname
itl.params['treeFormat'] = 'newick'
#===================================
# Check parameters
# itl.print_variables()
#Submit the tree
print('')
good_upload = itl.upload()
if good_upload == False:
print('There was an error:' + itl.comm.upload_output)
return 1
#Export to pdf
tree_id = itl.comm.tree_id
itol_exporter = itl.get_itol_export()
itol_exporter.set_export_param_value('format', "pdf")
itol_exporter.set_export_param_value(
'display_mode', "1") #(1=normal, 2=circular, 3=unrooted)
itol_exporter.set_export_param_value('line_width', "1")
#epsfile = outpath + os.sep + rootname + '.itolnormal.eps'
pdffile = outpath + os.sep + rootname + '.itolnormal.pdf'
print('Exporting to pdffile %s' % (pdffile))
itol_exporter.export(pdffile)
orderfile = outpath + os.sep + rootname + '.listorder.txt'
os.system("pdftotext -nopgbrk %s %s" % (pdffile, orderfile))
os.system("rm -f %s" % pdffile)
print('list order output to ', orderfile)
class ItolTest(unittest.TestCase):
def setUp(self):
self.itol = Itol()
def test_initializes(self):
self.assertEqual(type(self.itol.params), dict)
self.assertEqual(self.itol.files, [])
self.assertIsNotNone(self.itol.comm)
def test_add_file(self):
with tempfile.NamedTemporaryFile() as temp:
self.itol.add_file(temp.name)
with self.assertRaises(IOError):
self.itol.add_file(' ')
def test_good_upload(self):
with patch('itolapi.Comm.upload_tree') as mock_upload:
mock_upload.return_value = True
self.itol.comm.tree_id = 1234
self.assertEqual(self.itol.upload(), 1234)
def test_bad_upload(self):
with patch('itolapi.Comm.upload_tree') as mock_upload:
mock_upload.return_value = False
self.itol.comm.tree_id = 1234
self.assertEqual(self.itol.upload(), 0)
def test_get_webpage(self):
self.itol.comm.tree_id = 'asdf'
webpage = self.itol.get_webpage()
self.assertIn('itol.embl.de', webpage)
self.assertIn('asdf', webpage)
def test_get_itol_export(self):
self.itol.comm.tree_id = 1234
export = self.itol.get_itol_export()
self.assertEqual(export.params['tree'], 1234)
@patch('itolapi.itol.pprint.pprint')
def test_print_variables(self, mock_print):
self.itol.params['treeName'] = 'test'
with tempfile.NamedTemporaryFile() as temp:
self.itol.add_file(temp.name)
self.itol.print_variables()
self.assertEqual(mock_print.call_args_list[0][0][0], self.itol.files)
self.assertEqual(mock_print.call_args_list[1][0][0], self.itol.params)
class ItolTest(unittest.TestCase):
def setUp(self):
self.itol = Itol()
def test_initializes(self):
self.assertEqual(type(self.itol.params), dict)
self.assertEqual(self.itol.files, [])
self.assertIsNotNone(self.itol.comm)
def test_add_file(self):
with tempfile.NamedTemporaryFile() as temp:
self.itol.add_file(temp.name)
with self.assertRaises(IOError):
self.itol.add_file(' ')
def test_good_upload(self):
with patch('itolapi.Comm.upload_tree') as mock_upload:
mock_upload.return_value = True
self.itol.comm.tree_id = 1234
self.assertEqual(self.itol.upload(), 1234)
def test_bad_upload(self):
with patch('itolapi.Comm.upload_tree') as mock_upload:
mock_upload.return_value = False
self.itol.comm.tree_id = 1234
self.assertEqual(self.itol.upload(), 0)
def test_get_webpage(self):
self.itol.comm.tree_id = 'asdf'
webpage = self.itol.get_webpage()
self.assertIn('itol.embl.de', webpage)
self.assertIn('asdf', webpage)
def test_get_itol_export(self):
self.itol.comm.tree_id = 1234
export = self.itol.get_itol_export()
self.assertEqual(export.params['tree'], 1234)
@patch('itolapi.itol.pprint.pprint')
def test_print_variables(self, mock_print):
self.itol.params['treeName'] = 'test'
with tempfile.NamedTemporaryFile() as temp:
self.itol.add_file(temp.name)
self.itol.print_variables()
self.assertEqual(mock_print.call_args_list[0][0][0], self.itol.files)
self.assertEqual(mock_print.call_args_list[1][0][0], self.itol.params)
def test_upload_download(self):
current_dir = os.path.dirname(os.path.realpath(__file__))
examples_dir = os.path.join(current_dir, '..', '..', 'examples')
test = Itol()
tree = os.path.join(examples_dir, 'tree_of_life.tree.txt')
test.add_file(tree)
dataset = os.path.join(examples_dir, 'colors_tol.txt')
test.add_file(dataset)
upload_status = test.upload()
self.assertTrue(upload_status)
exporter = test.get_itol_export()
exporter.set_export_param_value('format', 'pdf')
with tempfile.NamedTemporaryFile() as temp:
exporter.export(temp.name)
# Read the tree ID
print('Tree ID: ' + str(test.comm.tree_id))
# Read the iTOL API return statement
print('iTOL output: ' + str(test.comm.upload_output))
# Website to be redirected to iTOL tree
print('Tree Web Page URL: ' + test.get_webpage())
# Warnings associated with the upload
print('Warnings: ' + str(test.comm.warnings))
# Export a pre-made tree to pdf
itol_exporter = ItolExport()
itol_exporter.set_export_param_value('tree', '18793532031912684633930')
itol_exporter.set_export_param_value('format', 'pdf')
itol_exporter.set_export_param_value('datasetList', 'dataset1')
# itol_exporter.export('example_pdf.pdf')
# print('exported tree to ',export_location)
# Export the tree above to pdf
print('Exporting to pdf')
itol_exporter = test.get_itol_export()
export_location = os.path.join(current_dir, 'example_pdf.pdf')
itol_exporter.set_export_param_value('format', 'pdf')
itol_exporter.set_export_param_value('datasetList', 'dataset1')
itol_exporter.export(export_location)
print('exported tree to ', export_location)
sys.exit(1)
# Read the tree ID
print('Tree ID: ' + str(test.comm.tree_id))
# Read the iTOL API return statement
print('iTOL output: ' + str(test.comm.upload_output))
# Website to be redirected to iTOL tree
print('Tree Web Page URL: ' + test.get_webpage())
# Warnings associated with the upload
print('Warnings: ' + str(test.comm.warnings))
# Export a pre-made tree to pdf
#itol_exporter = ItolExport()
#itol_exporter.set_export_param_value('tree', '18793532031912684633930')
#itol_exporter.set_export_param_value('format', 'pdf')
#itol_exporter.set_export_param_value('datasetList', 'dataset1')
# itol_exporter.export('example_pdf.pdf')
# print('exported tree to ',export_location)
# Export the tree above to pdf
print('Exporting to pdf')
itol_exporter = test.get_itol_export()
export_location = os.path.join(current_dir, family_domain_ID + '_tree.pdf')
itol_exporter.set_export_param_value('format', 'pdf')
itol_exporter.set_export_param_value('datasetList', 'dataset1')
itol_exporter.export(export_location)
print('exported tree to ', export_location)
class ITOL():
"""
Tree with branch lengths::
(A:0.1,(B:0.1,C:0.1)));
Tree with bootstrap and branch lengths::
(A:0.1,(B:0.1,C:0.1)90:0.1)98:0.3);
.. plot::
from pylab import imshow, imread
from easydev import TempFile
from sequana import ITOL, sequana_data
itol = ITOL(sequana_data("test_itol_basic.tree.txt"))
itol.upload()
# You can change the parameters in itol.params
itol.params["display_mode"] = 1 # use linear layout instead of circular
# finally export your image locally:
with TempFile(suffix=".png") as fout:
itol.export(fout.name)
imshow(imread(fout.name))
"""
def __init__(self, tree):
self.itol = Itol()
assert tree.endswith(
".tree.txt"), "Your input tree must end in .tree.txt"
self.itol.add_file(tree)
self._datasets = 0
self.status = None
# datasets_visible should not be used if there is no datasets.
#
self.params = {
"display_mode": 2, # rotation
"ignore_branch_length": 1,
"line_width": 5,
#"datasets_visible": "0,1",
'bootstrap_display': 1,
'bootstrap_type': 2,
'bootstrap_label_size': 32
}
def add_file(self, filename):
self.itol.add_file(filename)
N = len(self.itol.files) - 1 # remove the input tree file
self.params['datasets_visible'] = ",".join(
[str(x) for x in range(0, N)])
def upload(self):
self.status = self.itol.upload()
assert self.status, "Something is wrong with your input tree"
def export(self, filename='test.png'):
if self.status is None:
logger.error("Upload the tree first with upload() method")
export = self.itol.get_itol_export()
# Set the format
if filename.endswith(".png"):
logger.info("Exporting in {} format".format("png"))
export.params['format'] = "png"
elif filename.endswith(".svg"):
logger.info("Exporting in {} format".format("svg"))
export.params['format'] = "svg"
elif filename.endswith(".pdf"):
logger.info("Exporting in {} format".format("pdf"))
export.params['format'] = "pdf"
elif filename.endswith(".eps"):
logger.info("Exporting in {} format".format("eps"))
export.params['format'] = "eps"
else:
raise ValueError("filename must end in pdf, png, svg or eps")
export.params.update(**self.params)
export.export(filename)
def Itol_Tree_m0(pfamid, datapath, outpath):#{{{
#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'
datafileList = [datafile1, datafile2, datafile3, datafile4, colordeffile, branchlabelfile]
rootname = os.path.basename(os.path.splitext(tree)[0])
#===================================
itl.add_file(tree)
itl.params['treeName'] = rootname
itl.params['treeFormat'] = 'newick'
valid_datafileList = []
for datafile in datafileList:
if os.path.exists(datafile):
itl.add_file(datafile)
valid_datafileList.append(datafile)
datasets_list = [str(x) for x in range(len(valid_datafileList))]
# 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', 'pdf')
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('datasets_visible',",".join(datasets_list))
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(pdffile)
#os.system("epstopdf %s" % epsfile )
os.system("convert %s %s" % (pdffile, jpgfile) )
os.system("convert -thumbnail 200 %s %s" % (jpgfile, thumbfile))
print('exported tree to ',pdffile)
def Itol_Tree_linear(treefile, fastafile, outpath):# {{{
"""
Generate itol tree linear
"""
if not treefile.endswith(".tree") or treefile.endswith(".tree.txt"):
newfile = treefile + ".tree"
shutil.copy2(treefile, newfile)
treefile = newfile
#Create the Itol class
itl = Itol()
#Set the tree file
tree = treefile
dirname = os.path.dirname(treefile)
if dirname == "":
dirname = "."
if outpath == "":
outpath = dirname
elif not os.path.exists(outpath):
os.system("mkdir -p %s"%(outpath))
rootname = os.path.basename(os.path.splitext(treefile)[0])
rtname_fastafile = os.path.basename(os.path.splitext(fastafile)[0])
colorragefile = dirname + os.sep + rtname_fastafile + ".colorrage.txt"
datafileList = [colorragefile]
if os.path.exists(fastafile):
cmd = "python %s/fasta2colorrange.py %s %s > %s"%(rundir, fastafile, treefile,colorragefile)
os.system(cmd)
#===================================
itl.add_file(tree)
itl.params['treeName'] = rootname
itl.params['treeFormat'] = 'newick'
valid_datafileList = []
for datafile in datafileList:
if os.path.exists(datafile):
itl.add_file(datafile)
valid_datafileList.append(datafile)
datasets_list = [str(x) for x in range(len(valid_datafileList))]
#===================================
# Check parameters
# itl.print_variables()
#Submit the tree
print('')
good_upload = itl.upload()
if good_upload == False:
print('There was an error:'+itl.comm.upload_output)
return 1
#Export to pdf
tree_id = itl.comm.tree_id
itol_exporter = itl.get_itol_export()
itol_exporter.set_export_param_value('format',"pdf")
itol_exporter.set_export_param_value('display_mode',"1") #(1=normal, 2=circular, 3=unrooted)
itol_exporter.set_export_param_value('line_width',"1")
#itol_exporter.set_export_param_value('align_labels',"1")
print(('datasets_visible',",".join(datasets_list)))
itol_exporter.set_export_param_value('datasets_visible',",".join(datasets_list))
#epsfile = outpath + os.sep + rootname + '.itolnormal.eps'
pdffile = outpath + os.sep + rootname + '.itol_linear.pdf'
print('Exporting to pdffile %s'%(pdffile))
itol_exporter.export(pdffile)
print(("Phylogenetic tree has been output to %s"%(pdffile)))
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_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_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_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)
# 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 = boom.upload()
if not good_upload:
print('There was an error:' + boom.comm.upload_output)
sys.exit(1)
# Read the tree ID
print('Tree ID: ' + str(boom.comm.tree_id))
# Read the iTOL API return statement
print('iTOL output: ' + str(boom.comm.upload_output))
# Website to be redirected to iTOL tree
print('Tree Web Page URL: ' + boom.get_webpage())
# Warnings associated with the upload
print('Warnings: ' + str(boom.comm.warnings))
# Export the tree to pdf
print('Exporting to pdf')
itol_exporter = boom.get_itol_export()
export_location = os.path.join(current_dir, 'MERS_CoV.pdf')
itol_exporter.set_export_param_value('format', 'pdf')
itol_exporter.set_export_param_value('datasetList', 'dataset1')
itol_exporter.export(export_location)
print('exported tree to ', export_location)