def get_orthologs_between_two_species_table(self,
taxid1,
taxid2,
csth=0.5,
elth=1):
"""Return formatted orthology table between two species """
#convert species names into taxid
if not str(taxid1).isdigit():
if not taxid1 in self.name2taxid:
return "Species %s have not been found!" % taxid1
taxid1 = self.name2taxid[taxid1]
if not str(taxid2).isdigit():
if not taxid2 in self.name2taxid:
return "Species %s have not been found!" % taxid2
taxid2 = self.name2taxid[taxid2]
htypetxt = "ortholog"
#add short species info ADD protein counts etc
header = self._get_genome_info(taxid1)
header += self._get_genome_info(taxid2)
#get orthologs
orthologs = self.get_orthologs_between_two_species(taxid1, taxid2)
##THIS IS MESSY BUT WORKING!
ocount = sum(len(o) for o in orthologs.itervalues())
p2count = {}
for o in filter(lambda x: len(x) == 1, orthologs.itervalues()):
p = o[0][0]
if p not in p2count:
p2count[p] = 1
else:
p2count[p] += 1
for o in filter(lambda x: len(x) > 1, orthologs.itervalues()):
for oi in o:
p = oi[0]
if p in p2count:
p2count[p] += 1
ocount_one2one = sum(c for p, c in p2count.iteritems() if c == 1)
header += "<b> %s orthologs of which %s are one-to-one.</b>" % (
locale.format("%d", ocount, grouping=True),
locale.format("%d", ocount_one2one, grouping=True))
#get orthologs
otable = orthologyTable()
#add header
colnames = ("<i>%s</i>"%self.get_spname(taxid1, 1), \
"<i>%s</i>"%self.get_spname(taxid2, 1), \
"CS", "EL", "Trees")+ self.TREES_REPOSITORIES_NAMES
widths = (120, 120, 0, 0,
0) + (0, ) * len(self.TREES_REPOSITORIES_NAMES)
for cell, width in zip(colnames, widths):
cell_class = td_flag = ""
if width:
td_flag = 'width="%s"' % width
otable.add_cell(0, cell, cell_class, td_flag)
#populate table
row_index = 1
for i, (prot1data, odata) in enumerate(orthologs.iteritems()):
#(metaid1, extid1)
metaid1 = int(prot1data.split('_')[0])
extid1 = "_".join(prot1data.split('_')[1:])
td_flag = 'rowspan="%s"' % len(odata)
cell_class = None
#use metaid if not external id
if not extid1 or extid1 == "None":
extid1 = self.id2str(metaid1, 0, 0)
#ortholog - popup on scroll over
if self.return_html:
protid1 = self.SEQLINKOR % (metaid1, metaid1, extid1, metaid1)
else:
protid1 = self.id2str(metaid1)
otable.add_cell(row_index, protid1, cell_class, td_flag)
#even or odd species row
if i % 2:
otable.tr_classes[row_index] = "even_row"
else:
otable.tr_classes[row_index] = "odd_row"
for metaid2, extid2, cs, el, trees, css in odata:
#use metaid if not external id
if not extid2:
extid2 = self.id2str(metaid2, 0, 0)
#ortholog - popup on scroll over
if self.return_html:
protid2 = self.SEQLINKOR % (metaid2, metaid2, extid2,
metaid2)
trees = self._add_link("%s|%s"%(self.id2str(metaid1), self.id2str(metaid2)), \
self.db['metaphors'][3], trees)
else:
protid2 = self.id2str(metaid2)
#protid2, CS, EL & trees
otable.add_cells(row_index, (protid2, "%.3f" % cs, el, trees))
#tree repository signals
for signal in css:
cell = cell_class = ""
if signal:
extcs, exttrees = signal
if exttrees > 1:
cell = "%.2f/%s" % (extcs, exttrees)
if extcs >= self.csth:
cell_class = "agreement"
else:
cell_class = "disagreement"
otable.add_cell(row_index, cell, cell_class)
row_index += 1
#return html-formatted
if self.return_html:
return header + otable.asHTML() + self.LEGEND
#OrthoXML to ADD
#TXT
else:
return otable.asTXT()
def get_orthologs_table(self, protid):
"""Return HTML or TXT formatted orthologs table"""
htypetxt = "ortholog"
#get metaid
metaid = self.get_metaid(protid)
##catch wrong protein ids here
if not metaid:
return "Your query produced no hits!"
#add short protein info
header = self.get_protein_info(metaid, 2)
#get orthologs
orthologs = self.get_orthologs(metaid)
if not orthologs:
return header + "<b>No %ss have been found.</b>" % htypetxt
header += "<b>%s %ss in %s species</b>\n"%(sum(len(o) for o in orthologs.itervalues()), \
htypetxt, len(orthologs))
out = []
otable = orthologyTable()
#add header
colnames = ("Target species", "Co-%ss"%htypetxt, "%ss"%htypetxt.capitalize(), \
"CS", "EL", "Trees")+ self.TREES_REPOSITORIES_NAMES
widths = (180, 120, 120, 0, 0,
0) + (0, ) * len(self.TREES_REPOSITORIES_NAMES)
for cell, width in zip(colnames, widths):
cell_class = td_flag = ""
if width:
td_flag = 'width="%s"' % width
otable.add_cell(0, cell, cell_class, td_flag)
#populate table
row_index = 1
taxids = sorted([t for t in orthologs if t in self.species],
key=lambda x: self.species[x][1])
for i, taxid in enumerate(taxids, 1):
td_flag = 'rowspan="%s"' % len(orthologs[taxid])
spname = self.species[taxid][1]
cell_class = None
otable.add_cell(row_index, spname, cell_class, td_flag)
#even or odd species row
if i % 2:
otable.tr_classes[row_index] = "even_row"
else:
otable.tr_classes[row_index] = "odd_row"
#add orthologs
for j, (metaid2, extid2, cs, el, trees, css,
coorths) in enumerate(orthologs[taxid], 1):
#use metaid if not external id
if not extid2:
extid2 = self.id2str(metaid2, 0, 0)
#co-orthology information
coorthologs = self.id2str(metaid, 0, 0) + " " + \
" ".join(self.id2str(coid, 0, 0) for coid, cocs in coorths)
#collapse co-orthologs if too many
if self.return_html and coorths:
coorthologs = """
<a onClick="javascript:togglecomments(\'i%s_j%s\')"> %s co-%ss</a>
<div id="i%s_j%s" class="commenthidden">%s</div>
</a>""" % (i, j, len(coorths) + 1, htypetxt, i, j, coorthologs)
otable.add_cell(row_index, coorthologs)
#ortholog - popup on scroll over
if self.return_html:
#protid2 = self._add_link(extid2, self.db['metaphors'][4])
protid2 = self.SEQLINKOR % (metaid2, metaid2, extid2,
metaid2)
trees = self._add_link("%s|%s"%(self.id2str(metaid), self.id2str(metaid2)), \
self.db['metaphors'][3], trees)
else:
protid2 = self.id2str(metaid2)
#protid2, CS, EL & trees
otable.add_cells(row_index, (protid2, "%.3f" % cs, el, trees))
#tree repository signals
for signal in css:
cell = cell_class = ""
if signal:
extcs, exttrees = signal
if exttrees > 1:
cell = "%.2f/%s" % (extcs, exttrees)
if extcs >= self.csth:
cell_class = "agreement"
else:
cell_class = "disagreement"
otable.add_cell(row_index, cell, cell_class)
row_index += 1
#return html-formatted
if self.return_html:
return header + otable.asHTML() + self.LEGEND
#OrthoXML to ADD
#TXT
else:
return otable.asTXT()
def get_trees(self, ids):
"""Return trees for protein IDs."""
out = []
if type(ids) is str:
ids = ids.split()
#get internal ids
metaids = [self.id2int(x) for x in ids if x and self.id2int(x)]
if not metaids:
return "Your query was not recognised!"
cmd = """SELECT name, www, protein_link, tree_link, extid, treeid
FROM protid2treeid WHERE protid=%s""" % metaids[0]
for i, metaid in enumerate(metaids):
out.append(self.get_protein_info(metaid, 3))
#limit by common with other metaids
if i:
cmd += " AND treeid IN (SELECT treeid FROM protid2treeid WHERE protid=%s)" % metaid
#remove repeats
cmd += " GROUP BY treeid"
results = self._fetch(cmd)
##format output
if len(metaids) > 1:
text = "<b><table><tr><td>Selected proteins are together %s</table></b>"
out.append(text % self.get_tree_info(metaids).lower())
if not results:
return "".join(out)
#process
db2trees = {}
for dbname, www, protein_link, tree_link, extid, treeid in results:
dblink = self._add_link('', www, dbname)
#add db
if dblink not in db2trees:
db2trees[dblink] = {}
#add extid
extid = self._add_link(extid, protein_link)
if extid not in db2trees[dblink]:
db2trees[dblink][extid] = []
#add trees
db2trees[dblink][extid].append(self._add_link(treeid, tree_link))
#get html
table = orthologyTable()
#add header
colnames = ("Database", "No. of trees", "External ID", "Trees")
widths = (80, 80, 120, 0)
for cell, width in zip(colnames, widths):
cell_class = td_flag = ""
if width:
td_flag = 'width="%s"' % width
table.add_cell(0, cell, cell_class, td_flag)
row_index = 1
for i, db in enumerate(sorted(db2trees), 1):
td_flag = 'rowspan="%s"' % len(db2trees[db])
#even or odd species row
if i % 2:
table.tr_classes[i] = "even_row"
else:
table.tr_classes[i] = "odd_row"
#add db & tree count cell
cell_class = None
table.add_cell(row_index, db, cell_class, td_flag)
table.add_cell(row_index,
sum(len(x) for x in db2trees[db].itervalues()),
cell_class, td_flag)
#add extid & trees
for extid, trees in sorted(db2trees[db].iteritems()):
table.add_cell(row_index, extid)
table.add_cell(
row_index, "<div id='scrollcell'>" +
", ".join(sorted(trees)) + "</div>")
row_index += 1
if self.return_html:
return "<br />".join(out) + table.asHTML()
else:
return "\n#".join(out) + table.asTXT()
def get_orthologs_between_two_species_table(self, taxid1, taxid2, csth=0.5, elth=1):
"""Return formatted orthology table between two species """
#convert species names into taxid
if not str(taxid1).isdigit():
if not taxid1 in self.name2taxid:
return "Species %s have not been found!"%taxid1
taxid1 = self.name2taxid[taxid1]
if not str(taxid2).isdigit():
if not taxid2 in self.name2taxid:
return "Species %s have not been found!"%taxid2
taxid2 = self.name2taxid[taxid2]
htypetxt = "ortholog"
#add short species info ADD protein counts etc
header = self._get_genome_info(taxid1)
header += self._get_genome_info(taxid2)
#get orthologs
orthologs = self.get_orthologs_between_two_species(taxid1, taxid2)
##THIS IS MESSY BUT WORKING!
ocount = sum(len(o) for o in orthologs.itervalues())
p2count = {}
for o in filter(lambda x: len(x)==1, orthologs.itervalues()):
p = o[0][0]
if p not in p2count:
p2count[p] = 1
else:
p2count[p] += 1
for o in filter(lambda x: len(x)>1, orthologs.itervalues()):
for oi in o:
p = oi[0]
if p in p2count:
p2count[p] += 1
ocount_one2one = sum(c for p, c in p2count.iteritems() if c==1)
header += "<b> %s orthologs of which %s are one-to-one.</b>"%(locale.format("%d", ocount, grouping=True), locale.format("%d", ocount_one2one, grouping=True))
#get orthologs
otable = orthologyTable()
#add header
colnames = ("<i>%s</i>"%self.get_spname(taxid1, 1), \
"<i>%s</i>"%self.get_spname(taxid2, 1), \
"CS", "EL", "Trees")+ self.TREES_REPOSITORIES_NAMES
widths = (120, 120, 0, 0, 0) + (0,)*len(self.TREES_REPOSITORIES_NAMES)
for cell, width in zip(colnames, widths):
cell_class = td_flag = ""
if width:
td_flag = 'width="%s"'%width
otable.add_cell(0, cell, cell_class, td_flag)
#populate table
row_index = 1
for i, (prot1data, odata) in enumerate(orthologs.iteritems()):
#(metaid1, extid1)
metaid1 = int(prot1data.split('_')[0])
extid1 = "_".join(prot1data.split('_')[1:])
td_flag = 'rowspan="%s"' % len(odata)
cell_class = None
#use metaid if not external id
if not extid1 or extid1=="None":
extid1 = self.id2str(metaid1, 0, 0)
#ortholog - popup on scroll over
if self.return_html:
protid1 = self.SEQLINKOR % (metaid1, metaid1, extid1, metaid1)
else:
protid1 = self.id2str(metaid1)
otable.add_cell(row_index, protid1, cell_class, td_flag)
#even or odd species row
if i%2:
otable.tr_classes[row_index] = "even_row"
else:
otable.tr_classes[row_index] = "odd_row"
for metaid2, extid2, cs, el, trees, css in odata:
#use metaid if not external id
if not extid2:
extid2 = self.id2str(metaid2, 0, 0)
#ortholog - popup on scroll over
if self.return_html:
protid2 = self.SEQLINKOR % (metaid2, metaid2, extid2, metaid2)
trees = self._add_link("%s|%s"%(self.id2str(metaid1), self.id2str(metaid2)), \
self.db['metaphors'][3], trees)
else:
protid2 = self.id2str(metaid2)
#protid2, CS, EL & trees
otable.add_cells(row_index, (protid2, "%.3f"%cs, el, trees))
#tree repository signals
for signal in css:
cell = cell_class = ""
if signal:
extcs, exttrees = signal
if exttrees>1:
cell = "%.2f/%s" % (extcs, exttrees)
if extcs >= self.csth:
cell_class = "agreement"
else:
cell_class = "disagreement"
otable.add_cell(row_index, cell, cell_class)
row_index += 1
#return html-formatted
if self.return_html:
return header + otable.asHTML() + self.LEGEND
#OrthoXML to ADD
#TXT
else:
return otable.asTXT()
def get_orthologs_table(self, protid):
"""Return HTML or TXT formatted orthologs table"""
htypetxt = "ortholog"
#get metaid
metaid = self.get_metaid(protid)
##catch wrong protein ids here
if not metaid:
return "Your query produced no hits!"
#add short protein info
header = self.get_protein_info(metaid, 2)
#get orthologs
orthologs = self.get_orthologs(metaid)
if not orthologs:
return header+"<b>No %ss have been found.</b>"%htypetxt
header += "<b>%s %ss in %s species</b>\n"%(sum(len(o) for o in orthologs.itervalues()), \
htypetxt, len(orthologs))
out = []
otable = orthologyTable()
#add header
colnames = ("Target species", "Co-%ss"%htypetxt, "%ss"%htypetxt.capitalize(), \
"CS", "EL", "Trees")+ self.TREES_REPOSITORIES_NAMES
widths = (180, 120, 120, 0, 0, 0) + (0,)*len(self.TREES_REPOSITORIES_NAMES)
for cell, width in zip(colnames, widths):
cell_class = td_flag = ""
if width:
td_flag = 'width="%s"'%width
otable.add_cell(0, cell, cell_class, td_flag)
#populate table
row_index = 1
taxids = sorted([t for t in orthologs if t in self.species], key=lambda x: self.species[x][1])
for i, taxid in enumerate(taxids, 1):
td_flag = 'rowspan="%s"' % len(orthologs[taxid])
spname = self.species[taxid][1]
cell_class = None
otable.add_cell(row_index, spname, cell_class, td_flag)
#even or odd species row
if i%2:
otable.tr_classes[row_index] = "even_row"
else:
otable.tr_classes[row_index] = "odd_row"
#add orthologs
for j, (metaid2, extid2, cs, el, trees, css, coorths) in enumerate(orthologs[taxid], 1):
#use metaid if not external id
if not extid2:
extid2 = self.id2str(metaid2, 0, 0)
#co-orthology information
coorthologs = self.id2str(metaid, 0, 0) + " " + \
" ".join(self.id2str(coid, 0, 0) for coid, cocs in coorths)
#collapse co-orthologs if too many
if self.return_html and coorths:
coorthologs = """
<a onClick="javascript:togglecomments(\'i%s_j%s\')"> %s co-%ss</a>
<div id="i%s_j%s" class="commenthidden">%s</div>
</a>""" % (i, j, len(coorths)+1, htypetxt, i, j, coorthologs)
otable.add_cell(row_index, coorthologs)
#ortholog - popup on scroll over
if self.return_html:
#protid2 = self._add_link(extid2, self.db['metaphors'][4])
protid2 = self.SEQLINKOR % (metaid2, metaid2, extid2, metaid2)
trees = self._add_link("%s|%s"%(self.id2str(metaid), self.id2str(metaid2)), \
self.db['metaphors'][3], trees)
else:
protid2 = self.id2str(metaid2)
#protid2, CS, EL & trees
otable.add_cells(row_index, (protid2, "%.3f"%cs, el, trees))
#tree repository signals
for signal in css:
cell = cell_class = ""
if signal:
extcs, exttrees = signal
if exttrees>1:
cell = "%.2f/%s" % (extcs, exttrees)
if extcs >= self.csth:
cell_class = "agreement"
else:
cell_class = "disagreement"
otable.add_cell(row_index, cell, cell_class)
row_index += 1
#return html-formatted
if self.return_html:
return header + otable.asHTML() + self.LEGEND
#OrthoXML to ADD
#TXT
else:
return otable.asTXT()
def get_trees(self, ids):
"""Return trees for protein IDs."""
out = []
if type(ids) is str:
ids = ids.split()
#get internal ids
metaids = [self.id2int(x) for x in ids if x and self.id2int(x)]
if not metaids:
return "Your query was not recognised!"
cmd = """SELECT name, www, protein_link, tree_link, extid, treeid
FROM protid2treeid WHERE protid=%s"""%metaids[0]
for i, metaid in enumerate(metaids):
out.append(self.get_protein_info(metaid, 3))
#limit by common with other metaids
if i:
cmd += " AND treeid IN (SELECT treeid FROM protid2treeid WHERE protid=%s)"%metaid
#remove repeats
cmd += " GROUP BY treeid"
results = self._fetch(cmd)
##format output
if len(metaids)>1:
text = "<b><table><tr><td>Selected proteins are together %s</table></b>"
out.append(text%self.get_tree_info(metaids).lower())
if not results:
return "".join(out)
#process
db2trees = {}
for dbname, www, protein_link, tree_link, extid, treeid in results:
dblink = self._add_link('', www, dbname)
#add db
if dblink not in db2trees:
db2trees[dblink] = {}
#add extid
extid = self._add_link(extid, protein_link)
if extid not in db2trees[dblink]:
db2trees[dblink][extid] = []
#add trees
db2trees[dblink][extid].append(self._add_link(treeid, tree_link))
#get html
table = orthologyTable()
#add header
colnames = ("Database", "No. of trees", "External ID", "Trees")
widths = (80, 80, 120, 0)
for cell, width in zip(colnames, widths):
cell_class = td_flag = ""
if width:
td_flag = 'width="%s"'%width
table.add_cell(0, cell, cell_class, td_flag)
row_index = 1
for i, db in enumerate(sorted(db2trees), 1):
td_flag = 'rowspan="%s"' % len(db2trees[db])
#even or odd species row
if i%2:
table.tr_classes[i] = "even_row"
else:
table.tr_classes[i] = "odd_row"
#add db & tree count cell
cell_class = None
table.add_cell(row_index, db, cell_class, td_flag)
table.add_cell(row_index, sum(len(x) for x in db2trees[db].itervalues()), cell_class, td_flag)
#add extid & trees
for extid, trees in sorted(db2trees[db].iteritems()):
table.add_cell(row_index, extid)
table.add_cell(row_index, "<div id='scrollcell'>"+", ".join(sorted(trees))+"</div>")
row_index += 1
if self.return_html:
return "<br />".join(out) + table.asHTML()
else:
return "\n#".join(out) + table.asTXT()
