def rss2(feed, pretty_print=True):
indent = '\n ' if pretty_print else ''
indent2 = '\n ' if pretty_print else ''
rss = Element('rss', version='2.0')
rss.text = '\n ' if pretty_print else ''
channel = SubElement(rss, 'channel')
channel.text = indent
channel.tail = '\n' if pretty_print else ''
set_rss2_text(SubElement(channel, 'title'), feed.title)
set_rss2_text(SubElement(channel, 'description'), feed.subtitle or '')
SubElement(channel, 'link').text = feed.link
SubElement(channel, 'lastBuildDate').text = rss2_date(feed.updated)
if feed.language: SubElement(channel, 'language').text = feed.language
if feed.rights: SubElement(channel, 'copyright').text = feed.rights
if feed.logo:
image = SubElement(channel, 'image')
image.text = indent2
SubElement(image, 'url').text = feed.logo
SubElement(image, 'title').text = ''
SubElement(image, 'link').text = feed.link
for child in image: child.tail = indent2
image[-1].tail = '\n ' if pretty_print else ''
for entry in feed.entries:
item = entry.rss2(pretty_print)
item[-1].tail = indent
channel.append(item)
for child in channel: child.tail = indent
channel[-1].tail = '\n ' if pretty_print else ''
return rss
def makerss(titletext, top, root, files):
print 'Building %s' % os.path.join(root, 'photos.rss')
dirlen = len(top) + len(os.path.sep)
rootpath = root[dirlen:]
rootlen = len(rootpath) > 0 and len(rootpath) + len(os.path.sep) or 0
rss = Element('rss', version='2.0')
rss.attrib['xmlns:atom'] = NS_ATOM
rss.attrib['xmlns:media'] = NS_MEDIA
channel = SubElement(rss, 'channel')
title = SubElement(channel, 'title')
title.text = titletext
description = SubElement(channel, 'description')
description.text = _(
'This feed enables cooliris http://www.cooliris.com/ in your web browser'
)
channel.append(Comment('must have a link for rss'))
link = SubElement(channel, 'link')
link.text = 'http://localhost/'
result = []
for image in files:
imagepath = util.www_image_path(image, '.images')
if not options.noimages:
util.www_image_create(os.path.join(top, image),
force=options.force,
verbose=options.verbose)
thumbpath = util.www_image_path(image, '.thumbs')
if not options.nothumbs:
util.www_thumb_create(os.path.join(top, image),
force=options.force,
verbose=options.verbose)
if options.verbose >= 3:
print 'rootpath:', rootpath, 'image:', image, 'imagepath:', imagepath, 'thumbpath:', thumbpath
print 'imagepath[rootlen:]:', imagepath[
rootlen:], 'thumbpath[rootlen:]:', thumbpath[rootlen:]
result.append(os.path.join(rootpath, image))
image = image[rootlen:]
item = SubElement(channel, 'item')
title = SubElement(item, 'title')
title.text = image
link = SubElement(item, 'link')
link.text = urllib.quote(imagepath)
description = SubElement(item, 'media:description')
description.text = convert_entities(
os.path.splitext(os.path.basename(image))[0])
# need to double quote special characters
thumbnail = SubElement(item,
'media:thumbnail',
url=urllib.quote(
urllib.quote(thumbpath[rootlen:])))
content = SubElement(item,
'media:content',
url=urllib.quote(urllib.quote(
imagepath[rootlen:])))
indent(rss)
file = open(os.path.join(root, 'photos.rss'), 'w')
print >> file, '<?xml version="1.0" encoding="UTF-8" standalone="yes"?>'
print >> file, tostring(rss)
file.close()
return result
def _create_embedded_devices(self):
if self.device.is_root_device():
embedded_devices = self.device.devices
if len(embedded_devices) > 0:
device_list_element = SubElement(self.device_element,
"deviceList")
for embedded_device in embedded_devices.values():
embedded_device_description = DeviceXMLGenerator(
embedded_device)
device_list_element.append(
embedded_device_description.generate())
def _create_embedded_devices(self):
if self.device.is_root_device():
embedded_devices = self.device.devices
if len(embedded_devices) > 0:
device_list_element = SubElement(self.device_element,
"deviceList")
for embedded_device in embedded_devices.values():
embedded_device_description = DeviceXMLGenerator(
embedded_device)
device_list_element.append(embedded_device_description.
generate())
def test_writer(self):
a = Element('a')
b = SubElement(a, 'b')
b.append(Comment('a comment'))
c = SubElement(b, 'c', d = 'e')
f = SubElement(c, 'f')
f.text = 'g'
h = SubElement(c, 'h')
h.text = 'i << >> << &&'
b.append(ProcessingInstruction('pdk', 'processing instruction'))
tree = ElementTree(a)
output = stringio()
write_pretty_xml(tree, output)
self.assert_equals_long(expected_xml_output, output.getvalue())
def gpx(self,gpx):
"Construct an ElementTree for the given GPX file"
root = Element("gpx",xmlns=NS,version="1.1",creator=self.creator)
for wpt in gpx.waypoints:
root.append(self.wpt(wpt,"wpt"))
for route in gpx.routes:
el = self.path(route,"rte","rtept")
xmlutil.write(el,route,Route._scheme)
root.append(el)
for track in gpx.tracks:
el = SubElement(root,"trk")
xmlutil.write(el,track,Track._scheme)
for seg in track:
el.append(self.path(seg,"trkseg","trkpt"))
return root
def makerss(titletext, top, root, files):
print 'Building %s' % os.path.join(root, 'photos.rss')
dirlen = len(top)+len(os.path.sep)
rootpath = root[dirlen:]
rootlen = len(rootpath) > 0 and len(rootpath)+len(os.path.sep) or 0
rss = Element('rss', version='2.0')
rss.attrib['xmlns:atom'] = NS_ATOM
rss.attrib['xmlns:media'] = NS_MEDIA
channel = SubElement(rss, 'channel')
title = SubElement(channel, 'title')
title.text = titletext
description = SubElement(channel, 'description')
description.text = _('This feed enables cooliris http://www.cooliris.com/ in your web browser')
channel.append(Comment('must have a link for rss'))
link = SubElement(channel, 'link')
link.text = 'http://localhost/'
result = []
for image in files:
imagepath = util.www_image_path(image, '.images')
if not options.noimages:
util.www_image_create(os.path.join(top, image), force=options.force, verbose=options.verbose)
thumbpath = util.www_image_path(image, '.thumbs')
if not options.nothumbs:
util.www_thumb_create(os.path.join(top, image), force=options.force, verbose=options.verbose)
if options.verbose >= 3:
print 'rootpath:', rootpath, 'image:', image, 'imagepath:', imagepath, 'thumbpath:', thumbpath
print 'imagepath[rootlen:]:', imagepath[rootlen:], 'thumbpath[rootlen:]:', thumbpath[rootlen:]
result.append(os.path.join(rootpath, image))
image = image[rootlen:]
item = SubElement(channel, 'item')
title = SubElement(item, 'title')
title.text = image
link = SubElement(item, 'link')
link.text = urllib.quote(imagepath)
description = SubElement(item, 'media:description')
description.text = convert_entities(os.path.splitext(os.path.basename(image))[0])
# need to double quote special characters
thumbnail = SubElement(item, 'media:thumbnail', url=urllib.quote(urllib.quote(thumbpath[rootlen:])))
content = SubElement(item, 'media:content', url=urllib.quote(urllib.quote(imagepath[rootlen:])))
indent(rss)
file = open(os.path.join(root, 'photos.rss'), 'w')
print >>file, '<?xml version="1.0" encoding="UTF-8" standalone="yes"?>'
print >>file, tostring(rss)
file.close()
return result
def rss2(feed, pretty_print=True):
indent = '\n ' if pretty_print else ''
indent2 = '\n ' if pretty_print else ''
rss = Element('rss', version='2.0')
rss.text = '\n ' if pretty_print else ''
channel = SubElement(rss, 'channel')
channel.text = indent
channel.tail = '\n' if pretty_print else ''
set_rss2_text(SubElement(channel, 'title'), feed.title)
set_rss2_text(SubElement(channel, 'description'), feed.subtitle or '')
SubElement(channel, 'link').text = feed.link
SubElement(channel, 'lastBuildDate').text = rss2_date(feed.updated)
if feed.language: SubElement(channel, 'language').text = feed.language
if feed.rights: SubElement(channel, 'copyright').text = feed.rights
if feed.logo:
image = SubElement(channel, 'image')
image.text = indent2
SubElement(image, 'url').text = feed.logo
SubElement(image, 'title').text = ''
SubElement(image, 'link').text = feed.link
for child in image:
child.tail = indent2
image[-1].tail = '\n ' if pretty_print else ''
for entry in feed.entries:
item = entry.rss2(pretty_print)
item[-1].tail = indent
channel.append(item)
for child in channel:
child.tail = indent
channel[-1].tail = '\n ' if pretty_print else ''
return rss
def apply_msgfdb(in_file, msms_run_summary, modifications, num_mods):
""" Read output file of MS-GFDB and add child elements to msms_run_summary """
spectrum2element = {}
enzyme_list = [ArgC,LysC,Trypsin,LysCP,Chymotrypsin,TrypChymo,TrypsinP,PepsinA,
CNBr,V8E,AspN,Formic_acid,AspNambic,V8DE]
semi_list = []
sample_enzyme = msms_run_summary.find('sample_enzyme')
for f in read_msgfdb(in_file):
spectrum = '%(name)s.%(scan)05i.%(scan)05i.%(charge)i' % \
{'name': remove_file_extention(f['#SpecFile']),
'scan': f['Scan#'], 'charge': f['Charge']}
enzyme_list, semi_list = what_enzyme(enzyme_list, semi_list, f['Peptide'])
peptide_prev_aa = f['Peptide'][0]
if peptide_prev_aa == '_':
peptide_prev_aa = '-'
peptide_middle = f['Peptide'][2:-2]
peptide_next_aa = f['Peptide'][-1]
if peptide_next_aa == '_':
peptide_next_aa = '-'
if ' ' in f['Protein']:
protein_name, protein_descr = f['Protein'].split(' ', 1)
else:
protein_name = f['Protein']
protein_descr = ''
precursor_neutral_mass = f['Precursor'] * f['Charge'] - f['Charge'] * H_plus
if spectrum not in spectrum2element:
spectrum_query = SubElement(msms_run_summary, 'spectrum_query')
spectrum2element[spectrum] = spectrum_query
spectrum_query.append(Element('search_result'))
spectrum_query.set('spectrum', spectrum)
spectrum_query.set('start_scan', str(f['Scan#']))
spectrum_query.set('end_scan', str(f['Scan#']))
spectrum_query.set('assumed_charge', str(f['Charge']))
spectrum_query.set('precursor_neutral_mass', str(precursor_neutral_mass))
spectrum_query = spectrum2element[spectrum]
search_result = spectrum_query.find('search_result')
search_hit = SubElement(search_result, 'search_hit')
search_hit.set('peptide', "".join(aa for aa in peptide_middle if aa.isalpha()))
search_hit.set('peptide_prev_aa', peptide_prev_aa)
search_hit.set('peptide_next_aa', peptide_next_aa)
search_hit.set('protein', protein_name)
search_hit.set('protein_descr', protein_descr)
modification_instances = sum((find_modifications(mod, peptide_middle) for mod in modifications), [])
calc_neutral_pep_mass = modified_peptide_mass(modification_instances, peptide_middle, num_mods)
if modification_instances:
modification_info = SubElement(search_hit, 'modification_info')
for mass, mass_diff, aa_number, is_opt in modification_instances:
maam = SubElement(modification_info, 'mod_aminoacid_mass')
maam.set('position', str(aa_number))
maam.set('mass', str(mass))
search_hit.set('calc_neutral_pep_mass', str(calc_neutral_pep_mass))
search_hit.set('massdiff', str(precursor_neutral_mass - calc_neutral_pep_mass))
for field in score_fields:
if field in f:
SubElement(search_hit, 'search_score', name=field, value=f[field])
# sample_enzyme.set('fidelity',flag)
if enzyme_list == []:
if semi_list == []:
sample_enzyme.set('name','NoEnzyme')
sample_enzyme.set('fidelity','nonspecific')
else:
sample_enzyme.set('fidelity','semispecific')
enzyme = re.split("\|",enzyme2name[re.search(r'<(\w+)>',semi_list[0][0]).group(1)])
else:
sample_enzyme.set('fidelity','specific')
enzyme = re.split("\|",enzyme2name[re.search(r'<(\w+)>',enzyme_list[0][0]).group(1)])
if not(enzyme_list == [] and semi_list == []):
sample_enzyme.set('name',enzyme[0])
specificity = SubElement(sample_enzyme, 'specificity')
specificity.set('cut',enzyme[1])
if enzyme[2]:
specificity.set('no_cut',enzyme[2])
specificity.set('sense',enzyme[3])
class Document(object):
"""building output waebric xhtml document """
def __init__(self, output, verbose=False):
self.lastElement = Element('html')
self.tree = ET.ElementTree(self.lastElement)
self.trees = [self.tree]
self.output = output
self.verbose = verbose
#@trace
def addElement(self, name):
self.lastElement = SubElement(self.lastElement, name)
return self.lastElement
#@trace
def addText(self, string):
if not len(self.lastElement):
e = self.lastElement
txt = "%s%s" % (e.text, string) if e.text else string
e.text = txt
else:
e = self.lastElement[-1]
txt = "%s%s" % (e.tail, string) if e.tail else string
e.tail = txt
def addAttribute(self,name,value):
if self.lastElement.get(name):
value = "%s %s" % (self.lastElement.get(name),value)
self.lastElement.set(name, value)
def addComment(self, string):
self.lastElement.append(ET.Comment(string))
def getFile(self, filename):
if self.output:
filename = "%s/%s" % (self.output, filename)
try:
_file = open(filename,'w')
except IOError:
print "file name %s cannot be opened, no output written" % filename
return
return _file
def setGoodRootElement(self):
"""make sure we have the correct root ellement according to the
wae standard. It could be needed to remove the top html
element because i ad it to work correctly with elementtree Libary.
"""
r = self.tree.getroot()
if len(r) == 1 and not r.text and not r[-1].tail:
child = r.getchildren()[0]
if isinstance(child.tag, str):#check needed for comment element.
self.tree._setroot(r[0])
def writeOutput(self, filename):
self.setGoodRootElement()
_file = self.getFile(filename)
DTD = """<?xml version="1.0" encoding="UTF-8"?>\n"""
_file.write(DTD)
for tree in self.trees:
if isinstance(tree, ET.ElementTree):
self.tree.write(_file)
else: #could be data string.
_file.write(tree)
_file.write('\n')
_file.close()
if self.verbose:
output = open(_file.name)
print output.read()
def writeEmptyFile(self, filename):
_file = self.getFile(filename)
_file.write('')
_file.close()
def apply_msgfdb(in_file, msms_run_summary, modifications, num_mods):
""" Read output file of MS-GFDB and add child elements to msms_run_summary """
spectrum2element = {}
enzyme_list = [
ArgC, LysC, Trypsin, LysCP, Chymotrypsin, TrypChymo, TrypsinP, PepsinA,
CNBr, V8E, AspN, Formic_acid, AspNambic, V8DE
]
semi_list = []
sample_enzyme = msms_run_summary.find('sample_enzyme')
for f in read_msgfdb(in_file):
spectrum = '%(name)s.%(scan)05i.%(scan)05i.%(charge)i' % \
{'name': remove_file_extention(f['#SpecFile']),
'scan': f['Scan#'], 'charge': f['Charge']}
enzyme_list, semi_list = what_enzyme(enzyme_list, semi_list,
f['Peptide'])
peptide_prev_aa = f['Peptide'][0]
if peptide_prev_aa == '_':
peptide_prev_aa = '-'
peptide_middle = f['Peptide'][2:-2]
peptide_next_aa = f['Peptide'][-1]
if peptide_next_aa == '_':
peptide_next_aa = '-'
if ' ' in f['Protein']:
protein_name, protein_descr = f['Protein'].split(' ', 1)
else:
protein_name = f['Protein']
protein_descr = ''
precursor_neutral_mass = f['Precursor'] * f['Charge'] - f[
'Charge'] * H_plus
if spectrum not in spectrum2element:
spectrum_query = SubElement(msms_run_summary, 'spectrum_query')
spectrum2element[spectrum] = spectrum_query
spectrum_query.append(Element('search_result'))
spectrum_query.set('spectrum', spectrum)
spectrum_query.set('start_scan', str(f['Scan#']))
spectrum_query.set('end_scan', str(f['Scan#']))
spectrum_query.set('assumed_charge', str(f['Charge']))
spectrum_query.set('precursor_neutral_mass',
str(precursor_neutral_mass))
spectrum_query = spectrum2element[spectrum]
search_result = spectrum_query.find('search_result')
search_hit = SubElement(search_result, 'search_hit')
search_hit.set('peptide',
"".join(aa for aa in peptide_middle if aa.isalpha()))
search_hit.set('peptide_prev_aa', peptide_prev_aa)
search_hit.set('peptide_next_aa', peptide_next_aa)
search_hit.set('protein', protein_name)
search_hit.set('protein_descr', protein_descr)
modification_instances = sum((find_modifications(mod, peptide_middle)
for mod in modifications), [])
calc_neutral_pep_mass = modified_peptide_mass(modification_instances,
peptide_middle, num_mods)
if modification_instances:
modification_info = SubElement(search_hit, 'modification_info')
for mass, mass_diff, aa_number, is_opt in modification_instances:
maam = SubElement(modification_info, 'mod_aminoacid_mass')
maam.set('position', str(aa_number))
maam.set('mass', str(mass))
search_hit.set('calc_neutral_pep_mass', str(calc_neutral_pep_mass))
search_hit.set('massdiff',
str(precursor_neutral_mass - calc_neutral_pep_mass))
for field in score_fields:
if field in f:
SubElement(search_hit,
'search_score',
name=field,
value=f[field])
# sample_enzyme.set('fidelity',flag)
if enzyme_list == []:
if semi_list == []:
sample_enzyme.set('name', 'NoEnzyme')
sample_enzyme.set('fidelity', 'nonspecific')
else:
sample_enzyme.set('fidelity', 'semispecific')
enzyme = re.split(
"\|", enzyme2name[re.search(r'<(\w+)>',
semi_list[0][0]).group(1)])
else:
sample_enzyme.set('fidelity', 'specific')
enzyme = re.split(
"\|", enzyme2name[re.search(r'<(\w+)>',
enzyme_list[0][0]).group(1)])
if not (enzyme_list == [] and semi_list == []):
sample_enzyme.set('name', enzyme[0])
specificity = SubElement(sample_enzyme, 'specificity')
specificity.set('cut', enzyme[1])
if enzyme[2]:
specificity.set('no_cut', enzyme[2])
specificity.set('sense', enzyme[3])
class Document(object):
"""building output waebric xhtml document """
def __init__(self, output, verbose=False):
self.lastElement = Element('html')
self.tree = ET.ElementTree(self.lastElement)
self.trees = [self.tree]
self.output = output
self.verbose = verbose
#@trace
def addElement(self, name):
self.lastElement = SubElement(self.lastElement, name)
return self.lastElement
#@trace
def addText(self, string):
if not len(self.lastElement):
e = self.lastElement
txt = "%s%s" % (e.text, string) if e.text else string
e.text = txt
else:
e = self.lastElement[-1]
txt = "%s%s" % (e.tail, string) if e.tail else string
e.tail = txt
def addAttribute(self, name, value):
if self.lastElement.get(name):
value = "%s %s" % (self.lastElement.get(name), value)
self.lastElement.set(name, value)
def addComment(self, string):
self.lastElement.append(ET.Comment(string))
def getFile(self, filename):
if self.output:
filename = "%s/%s" % (self.output, filename)
try:
_file = open(filename, 'w')
except IOError:
print "file name %s cannot be opened, no output written" % filename
return
return _file
def setGoodRootElement(self):
"""make sure we have the correct root ellement according to the
wae standard. It could be needed to remove the top html
element because i ad it to work correctly with elementtree Libary.
"""
r = self.tree.getroot()
if len(r) == 1 and not r.text and not r[-1].tail:
child = r.getchildren()[0]
if isinstance(child.tag, str): #check needed for comment element.
self.tree._setroot(r[0])
def writeOutput(self, filename):
self.setGoodRootElement()
_file = self.getFile(filename)
DTD = """<?xml version="1.0" encoding="UTF-8"?>\n"""
_file.write(DTD)
for tree in self.trees:
if isinstance(tree, ET.ElementTree):
self.tree.write(_file)
else: #could be data string.
_file.write(tree)
_file.write('\n')
_file.close()
if self.verbose:
output = open(_file.name)
print output.read()
def writeEmptyFile(self, filename):
_file = self.getFile(filename)
_file.write('')
_file.close()
