def upload_to_itol(tree_path,
dataset_paths,
tree_name=None,
tree_description=None,
project_name=None,
upload_id=None):
try:
itol_uploader = Itol()
itol_uploader.add_file(tree_path)
for annotation_file in dataset_paths:
itol_uploader.add_file(annotation_file)
if tree_name:
itol_uploader.params['treeName'] = tree_name
if tree_description:
itol_uploader.params['treeDescription'] = tree_description
if upload_id:
itol_uploader.params['uploadID'] = upload_id
if project_name:
itol_uploader.params['projectName'] = project_name
if itol_uploader.upload():
logging.getLogger('pastml').debug(
'Successfully uploaded your tree ({}) to iTOL: {}.'.format(
itol_uploader.comm.tree_id, itol_uploader.get_webpage()))
return itol_uploader.comm.tree_id, itol_uploader.get_webpage()
else:
status = itol_uploader.comm.upload_output
except Exception as e:
status = e
logging.getLogger('pastml').error(
'Failed to upload your tree to iTOL because of "{}". Please check your internet connection and itol settings{}.'
.format(status, (', e.g. your iTOL batch upload id ({}){}'.format(
upload_id,
(' and whether the project {} exists'.format(project_name)
if project_name else ''))) if upload_id else ''))
return None, None
def create_itol_link(process_ID, newick):
with open(
"/home/ubuntu/coxbase/tools/grapeTree/tre/{}.tree".format(
process_ID),
"w",
encoding="utf-8",
) as open_file:
open_file.write(newick)
itol_uploader = Itol()
itol_uploader.add_file(
"/home/ubuntu/coxbase/tools/grapeTree/tre/{}.tree".format(
process_ID))
itol_uploader.params["treeName"] = process_ID
itol_uploader.upload()
return itol_uploader.get_webpage()
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)
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)
def visualize_itol(request, taxonomy_id):
newick_tree = services.newick_tree(taxonomy_id)
tree_fh = NamedTemporaryFile(mode='w', suffix='.tree')
tree_fh.write(newick_tree)
tree_fh.flush()
try:
from itolapi import Itol
itol_uploader = Itol()
itol_uploader.add_file(tree_fh.name)
status = itol_uploader.upload()
assert status != False
itol_page = itol_uploader.get_webpage()
return redirect(itol_uploader.get_webpage())
except:
return HttpResponse('Something went wrong with the iTOL API. Save the following Newick tree to a file and upload it to iTOL yourself to visualize the tree:\n{}'.format(newick_tree), content_type = "text/plain")
'''return HttpResponse(newick_tree)'''
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 plot(output_dir: str, table: biom.Table, tree: NewickFormat,
feature_metadata: pd.DataFrame, category: str,
color_palette: str = 'Dark2', ms2_label: bool = False,
parent_mz: str = None) -> None:
if category not in feature_metadata.columns:
raise ValueError('Could not find %s in the feature data, the available'
' columns are: %s.' %
(category,
', '.join(feature_metadata.columns.astype())))
color_fp = join(output_dir, 'colors.tsv')
with open(color_fp, 'w') as fh:
fh.write(format_colors(feature_metadata, category, color_palette))
label_fp = join(output_dir, 'labels.tsv')
with open(label_fp, 'w') as fh:
fh.write(format_labels(feature_metadata, category, ms2_label,
parent_mz))
# itol won't accept a file unless it has a .tree or .txt extension
target = join(output_dir, 'qemistree.tree')
copyfile(str(tree), target)
# upload the tree, labels and tip coloring files
itol_uploader = Itol()
itol_uploader.add_file(target)
itol_uploader.add_file(label_fp)
itol_uploader.add_file(color_fp)
status = itol_uploader.upload()
if not status:
raise ValueError(itol_uploader.comm.upload_output)
url = itol_uploader.get_webpage()
print(url)
index_path = join(TEMPLATES, 'index.html')
q2templates.render(index_path, output_dir, context={'url': url})
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 plot(output_dir: str,
tree: NewickFormat,
feature_metadata: pd.DataFrame,
category: str = 'class',
ms2_label: bool = False,
color_palette: str = 'Dark2',
parent_mz: bool = True,
grouped_table: biom.Table = None,
normalize_features: bool = True) -> None:
'''This function plots the phenetic tree in iTOL with clade colors,
feature labels and relative abundance per sample group.
Parameters
----------
tree : NewickFormat
Phenetic tree
feature_metadata : pd.DataFrame
Feature metadata
grouped_table : biom.Table, optional
Feature table of samples grouped by categories
category : str, optional
The feature data column used to color and label the tips.
Default 'class'
color_palette : str, optional
The color palette to use for coloring tips
ms2_label : bool, optional
Whether to label the tips with the MS2 value
parent_mz : bool, optional
If the feature is unclassified, label the tips using parent mass of
compound
normalize_features : bool, optional
If True (default), the feature abundances are normalized to
a constant sum i.e converted to relative abundances
Raises
------
ValueError
If `category` is not a column in `feature_metadata`
UserWarning
If the number of unique values in `category` is greater than the number
of unique colors in `color_palette`
Returns
-------
None
'''
if category not in feature_metadata.columns:
raise ValueError(
'Could not find %s in the feature data, the available'
' columns are: %s.' %
(category, ', '.join(feature_metadata.columns.astype())))
color_fp = join(output_dir, 'colors')
with open(color_fp, 'w') as fh:
fh.write(format_colors(feature_metadata, category, color_palette))
label_fp = join(output_dir, 'labels')
with open(label_fp, 'w') as fh:
fh.write(
format_labels(feature_metadata, category, ms2_label, parent_mz))
# itol won't accept a tree file unless it has a .tree or .txt extension
target = join(output_dir, 'qemistree.tree')
copyfile(str(tree), target)
# upload the tree, labels and tip coloring files
itol_uploader = Itol()
itol_uploader.add_file(target)
itol_uploader.add_file(label_fp)
itol_uploader.add_file(color_fp)
if grouped_table is not None:
barplot_fp = join(output_dir, 'barplots')
with open(barplot_fp, 'w') as fh:
fh.write(format_barplots(grouped_table, normalize_features))
itol_uploader.add_file(barplot_fp)
status = itol_uploader.upload()
if not status:
raise ValueError(itol_uploader.comm.upload_output)
url = itol_uploader.get_webpage()
print(url)
index_path = join(TEMPLATES, 'index.html')
q2templates.render(index_path,
output_dir,
context={
'url': url,
'has_barplots': grouped_table is not None
})
chosentree = args.tree
family_domain_ID = args.tree.split(".")[0]
current_dir = os.path.dirname(os.path.realpath(__file__))
root_path = os.path.join(current_dir, '..')
sys.path.append(root_path)
from itolapi import Itol, ItolExport # NOQA
print('Running example itol and itolexport script')
print('')
print('Creating the upload params')
# Create the Itol class
test = Itol()
# Set the tree file
tree = os.path.join(current_dir, args.tree)
test.add_file(tree)
test.add_file(os.path.join(current_dir, args.colour))
#test.add_file(os.path.join(current_dir, 'labels.txt'))
#test.add_file(os.path.join(current_dir, 'ranges.txt'))
# Add parameters
test.params['treeName'] = 'Tree File'
# Check parameters
test.print_variables()
# Submit the tree
print('')
print(
('Uploading the tree. This may take some time depending on how large the '
def upload_and_export_itol(
cassiopeia_tree: CassiopeiaTree,
tree_name: str,
export_filepath: str,
itol_config: str = "~/.itolconfig",
api_key: Optional[str] = None,
project_name: Optional[str] = None,
meta_data: List[str] = [],
allele_table: Optional[pd.DataFrame] = None,
indel_colors: Optional[pd.DataFrame] = None,
indel_priors: Optional[pd.DataFrame] = None,
rect: bool = False,
include_legend: bool = False,
use_branch_lengths: bool = False,
palette: List[str] = palettes.Category20[20],
random_state: Optional[np.random.RandomState] = None,
user_dataset_files: Optional[List[str]] = None,
verbose: bool = True,
**kwargs,
):
"""Uploads a tree to iTOL and exports it.
This function takes in a tree, plots it with iTOL, and exports it locally.
A user can also specify meta data and allele tables to visualize alongside
their tree. The function requires a user to have an account with iTOL and
can pass these credentials to the function in one of two ways: first, the
user can specify an `api_key` and a `project_name`, which corresponds to one
in the user's iTOL account' second, the user can have a hidden `itolconfig`
file that can store these credentials (the default location we will check
is in ~/.itolconfig, though this can be overridden by the user). We
preferentially take values passed in explicitly to the function in the
`api_key` and `project_name` arguments.
TODO(mgjones): Add the ability to pass in min/max colors for specific
numeric meta data to use when creating the gradient files.
Args:
cassiopeia_tree: A CassiopeiaTree instance, populated with a tree.
tree_name: Name of the tree. This is what the tree will be called
within your project directory on iTOL
export_filepath: Output file path to save your tree. Must end with
one of the following suffixes: ['png', 'svg', 'eps', 'ps', 'pdf'].
itol_config: A configuration file that a user can maintain for storing
iTOL account details (specifically, an API key and a project name
for uploading trees). We assume that the information is stored under
the [DEFAULT] header. We also will be default check the path
`~/itolconfig` but the user can pass in another path should they
wish. If an `api_key` and `project_name` are also passed in, we
will preferentially take those values.
api_key: API key linking to your iTOL account
project_name: Project name to upload to.
meta_data: Meta data to plot alongside the tree, which must be columns
in the CassiopeiaTree.cell_meta variable.
allele_table: Alleletable to plot alongside the tree.
indel_colors: Color mapping to use for plotting the alleles for each
cell. Only necessary if `allele_table` is specified.
indel_priors: Prior probabilities for each indel. Only useful if an
allele table is to be plotted and `indel_colors` is None.
rect: Boolean indicating whether or not to save your tree as a circle
or rectangle.
use_branch_lengths: Whether or not to use branch lengths when exporting
the tree.
include_legend: Plot legend along with meta data.
palette: A palette of colors in hex format.
random_state: A random state for reproducibility
user_dataset_files: List of paths to additional dataset files to upload.
See https://itol.embl.de/help.cgi#dsType for available dataset types
and their definitions.
verbose: Include extra print statements.
**kwargs: additional keyword arguments are passed as iTOL export parameters.
See https://itol.embl.de/help.cgi#batch for a full list.
Raises:
iTOLError if iTOL credentials cannot be found, if the output format is
not supported, if meta data to be plotted cannot be found, or if
an error with iTOL is encountered.
"""
# create temporary directory for storing files we'll upload to iTOL
temporary_directory = tempfile.mkdtemp()
if api_key is None or project_name is None:
if os.path.exists(os.path.expanduser(itol_config)):
config = configparser.ConfigParser()
with open(os.path.expanduser(itol_config), "r") as f:
config_string = f.read()
config.read_string(config_string)
try:
api_key = config["DEFAULT"]["api_key"]
project_name = config["DEFAULT"]["project_name"]
except KeyError:
raise iTOLError(
"Error reading the itol config file passed in.")
else:
raise iTOLError(
"Specify an api_key and project_name, or a valid iTOL "
"config file.")
with open(os.path.join(temporary_directory, "tree_to_plot.tree"),
"w") as f:
f.write(cassiopeia_tree.get_newick(record_branch_lengths=True))
file_format = export_filepath.split("/")[-1].split(".")[-1]
if file_format not in ["png", "svg", "eps", "ps", "pdf"]:
raise iTOLError("File format must be one of "
"'png', 'svg', 'eps', 'ps', 'pdf']")
itol_uploader = Itol()
itol_uploader.add_file(
os.path.join(temporary_directory, "tree_to_plot.tree"))
files = user_dataset_files.copy() if user_dataset_files else []
if allele_table is not None:
files += create_indel_heatmap(
allele_table,
cassiopeia_tree,
f"{tree_name}.allele",
temporary_directory,
indel_colors,
indel_priors,
random_state,
)
for meta_item in meta_data:
if meta_item not in cassiopeia_tree.cell_meta.columns:
raise iTOLError("Meta data item not in CassiopeiaTree cell meta.")
values = cassiopeia_tree.cell_meta[meta_item]
if pd.api.types.is_numeric_dtype(values):
files.append(
create_gradient_from_df(
values,
cassiopeia_tree,
f"{tree_name}.{meta_item}",
temporary_directory,
))
if pd.api.types.is_string_dtype(values):
colors = palette[:len(values.unique())]
colors = [utilities.hex_to_rgb(color) for color in colors]
colormap = dict(zip(np.unique(values), colors))
files.append(
create_colorbar(
values,
cassiopeia_tree,
colormap,
f"{tree_name}.{meta_item}",
temporary_directory,
create_legend=include_legend,
))
for _file in files:
itol_uploader.add_file(_file)
itol_uploader.params["treeName"] = tree_name
itol_uploader.params["APIkey"] = api_key
itol_uploader.params["projectName"] = project_name
good_upload = itol_uploader.upload()
if not good_upload:
raise iTOLError(itol_uploader.comm.upload_output)
if verbose:
print("iTOL output: " + str(itol_uploader.comm.upload_output))
print("Tree Web Page URL: " + itol_uploader.get_webpage())
print("Warnings: " + str(itol_uploader.comm.warnings))
tree_id = itol_uploader.comm.tree_id
itol_exporter = ItolExport()
# set parameters:
itol_exporter.set_export_param_value("tree", tree_id)
itol_exporter.set_export_param_value("format", file_format)
if rect:
# rectangular tree settings
itol_exporter.set_export_param_value("display_mode", 1)
else:
# circular tree settings
itol_exporter.set_export_param_value("display_mode", 2)
itol_exporter.set_export_param_value("arc", 359)
itol_exporter.set_export_param_value("rotation", 270)
itol_exporter.set_export_param_value("leaf_sorting", 1)
itol_exporter.set_export_param_value("label_display", 0)
itol_exporter.set_export_param_value("internal_marks", 0)
itol_exporter.set_export_param_value("ignore_branch_length",
1 - int(use_branch_lengths))
itol_exporter.set_export_param_value(
"datasets_visible", ",".join([str(i) for i in range(len(files))]))
itol_exporter.set_export_param_value("horizontal_scale_factor", 1)
for key, value in kwargs.items():
itol_exporter.set_export_param_value(key, value)
# export!
itol_exporter.export(export_filepath)
# remove intermediate files
shutil.rmtree(temporary_directory)
def setUp(self):
self.itol = Itol()
def upload_to_itol(
tree,
apiKey,
projectName,
tree_name="test",
files=[],
outfp="test.pdf",
fformat=None,
rect=False,
**kwargs,
):
_leaves = tree.get_leaf_names()
tree.write(outfile="tree_to_plot.tree", format=1)
if fformat is None:
fformat = outfp.split(".")[-1]
itol_uploader = Itol()
itol_uploader.add_file("tree_to_plot.tree")
for file in files:
itol_uploader.add_file(file)
itol_uploader.params["treeName"] = tree_name
itol_uploader.params["APIkey"] = apiKey
itol_uploader.params["projectName"] = projectName
good_upload = itol_uploader.upload()
if not good_upload:
print("There was an error:" + itol_uploader.comm.upload_output)
print("iTOL output: " + str(itol_uploader.comm.upload_output))
print("Tree Web Page URL: " + itol_uploader.get_webpage())
print("Warnings: " + str(itol_uploader.comm.warnings))
tree_id = itol_uploader.comm.tree_id
itol_exporter = ItolExport()
# set parameters:
itol_exporter.set_export_param_value("tree", tree_id)
itol_exporter.set_export_param_value(
"format",
outfp.split(
".")[-1]) # ['png', 'svg', 'eps', 'ps', 'pdf', 'nexus', 'newick']
if rect:
itol_exporter.set_export_param_value("display_mode",
1) # rectangular tree
else:
itol_exporter.set_export_param_value("display_mode",
2) # circular tree
itol_exporter.set_export_param_value("arc", 359)
itol_exporter.set_export_param_value("rotation", 270)
itol_exporter.set_export_param_value("leaf_sorting", 1)
itol_exporter.set_export_param_value("label_display", 1)
itol_exporter.set_export_param_value("internal_marks", 1)
itol_exporter.set_export_param_value("ignore_branch_length", 1)
itol_exporter.set_export_param_value(
"datasets_visible", ",".join([str(i) for i in range(len(files))]))
itol_exporter.set_export_param_value(
"horizontal_scale_factor", 1) # doesnt actually scale the artboard
# export!
itol_exporter.export(outfp)
os.remove("tree_to_plot.tree")
if args.root == 'midpoint':
root = '1'
else:
root = args.root
# Modify tree
cmd = 'java -Xmx16m -jar ~/bin/TreeCollapseCL4.jar -f %s -b %s -r %s' %(args.tree, args.boot, root)
os.system(cmd)
prefix, suffix = re.search('(.*?)\.(.*?)$', args.tree).groups()
tree = '%s_%scoll.%s' %(prefix, args.boot, suffix)
args.tree = '%s.tmp' %(args.tree)
cmd = 'mv %s %s' %(tree, args.tree)
os.system(cmd)
# Upload tree
uploader = Itol.Itol()
uploader.add_variable('treeFile', args.tree)
uploader.add_variable('treeFormat', 'newick')
uploader.add_variable('treeName', args.out)
if args.root == 'midpoint':
uploader.add_variable('midpointRoot', '1')
uploader.upload()
tree_id = uploader.comm.tree_id
# Export tree
exporter = ItolExport.ItolExport()
exporter.set_export_param_value('tree', tree_id)
exporter.set_export_param_value('format', 'pdf')
exporter.set_export_param_value('displayMode', args.mode)
exporter.export(args.out)
import os
import sys
pathname = os.path.dirname(sys.argv[0])
fullpath = os.path.abspath(pathname)
parent_path = fullpath + "/../../"
sys.path.append(parent_path)
from itolapi import Itol
parse_fn = 'huge.matrix.tree.parse'
color_fn = 'huge.matrix.tree.parse.color'
abun_fn = 'huge.matrix.tree.parse.abun'
itol_o = Itol.Itol()
itol_o.add_variable('treeFile', parse_fn)
itol_o.add_variable('treeName', 'HuGE Tree')
itol_o.add_variable('treeFormat', 'newick')
itol_o.add_variable('colorDefinitionFile', color_fn)
itol_o.add_variable('dataset1File', abun_fn)
itol_o.add_variable('dataset1Label', 'Abundance')
itol_o.add_variable('dataset1Separator', 'comma')
itol_o.add_variable('dataset1Type', 'multibar')
itol_o.add_variable('dataset1Color', '#ff0000')
itol_o.add_variable('dataset1MultiBarAlign', '1')
itol_o.add_variable('dataset1PieTransparent', '0')
itol_o.add_variable('dataset1PieRadiusMax', '100')
itol_o.add_variable('dataset1PieRadiusMin', '20')
itol_o.add_variable('dataset1BarSizeMax', '20')
itol_o.print_variables()
import os
import sys
pathname = os.path.dirname(sys.argv[0])
fullpath = os.path.abspath(pathname)
parent_path = fullpath + "/../"
sys.path.append(parent_path)
from itolapi import Itol, ItolExport
print('Running example itol and itolexport script')
print('')
print('Creating the upload params')
# Create the Itol class
test = Itol.Itol()
# Set the tree file
tree = fullpath + '/example_tree'
test.add_variable('treeFile', tree)
# Add parameters
test.add_variable('treeName', 'adsf')
test.add_variable('treeFormat', 'newick')
test.add_variable('dataset1File', fullpath + '/example_data')
test.add_variable('dataset1Label', 'colors')
test.add_variable('dataset1Separator', 'comma')
test.add_variable('dataset1Type', 'multibar')
# Check parameters
test.print_variables()
# Submit the tree
print('')
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)
import os
import sys
from itolapi import Itol, ItolExport
current_dir = os.path.dirname(os.path.realpath(__file__))
root_path = os.path.join(current_dir, '..')
sys.path.append(root_path)
boom = Itol()
# Set the tree file
tree = os.path.join(current_dir, 'MERS_CoV.tree.txt')
boom.add_file(tree)
# Add parameters
boom.params['treeName'] = 'MERS_CoV'
boom.params['display_mode'] = '2'
boom.params['ignore_branch_length'] = '1'
boom.params['current_font_size'] = '28'
# Check parameters
boom.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 = boom.upload()
if not good_upload:
print('There was an error:' + boom.comm.upload_output)
sys.exit(1)