def InferSingleLettterCode(threlettercode):
'''
Convert the amino acid three letter code, into a single letter code
'''
from tl.rename.case import transform_sentence_case
aa = {
'Gly': 'G',
'Ala': 'A',
'Val': 'V',
'Leu': 'L',
'Ile': 'I',
'Met': 'M',
'Phe': 'F',
'Trp': 'W',
'Pro': 'P',
'Ser': 'S',
'Thr': 'T',
'Cys': 'C',
'Tyr': 'Y',
'Asn': 'N',
'Gln': 'Q',
'Asp': 'D',
'Glu': 'E',
'Lys': 'K',
'Arg': 'R',
'His': 'H'
}
singleletter = aa[transform_sentence_case([threlettercode])[0]]
return singleletter
def clean_string(instr, change_case=True):
'''
Clean string: change \n to <br /> and escape ampersand
'''
cleaned_string = instr.replace('\n', '<br />').replace('&', '&')
if(get_config('clean_string_sentence_case') == 'True' and change_case):
cleaned_string = transform_sentence_case([cleaned_string])[0]
return cleaned_string
def InferSingleLettterCode(threlettercode):
'''
Convert the amino acid three letter code, into a single letter code
'''
from tl.rename.case import transform_sentence_case
aa = {'Gly':'G' , 'Ala':'A' , 'Val':'V' , 'Leu':'L' , 'Ile':'I' , 'Met':'M' , 'Phe':'F' ,
'Trp':'W' , 'Pro':'P' , 'Ser':'S' , 'Thr':'T' , 'Cys':'C' , 'Tyr':'Y' , 'Asn':'N' ,
'Gln':'Q' , 'Asp':'D' , 'Glu':'E' , 'Lys':'K' , 'Arg':'R' , 'His':'H'}
singleletter = aa[transform_sentence_case([threlettercode])[0]]
return singleletter
def report_qec_interest_areas(request):
# class ReportForm(forms.Form):
# semester = forms.ChoiceField(choices=SEMESTER_CHOICES)
# year = forms.CharField()
#
# c = RequestContext(request)
# c.update(csrf(request))
all_areas = {}
inst_areas = []
instructors = InstructorProfile.objects.all()
for i in instructors:
areas = i.areas_of_interest
inst_areas.append(['<b>' + unicode(i) + '</b> (' + i.designation + '): ', areas.strip().replace('\n', '; ')])
areas = re.split("\n", areas)
for a in areas:
if a.upper() != a: # leave all caps alone
a = a.strip().lower()
if a == '': continue
try:
all_areas[a] = all_areas[a] + 1
except:
all_areas[a] = 1
areas = {}
for area, count in all_areas.items():
if area.upper() != area: # leave all caps alone
area = transform_sentence_case([area])[0]
areas[area] = count
# prepare list of courses [{'Course Name' : course_name, 'Course Code' : course_name }
# , {...}]
return render_to_response('qec_interest_areas.html' , {
'areas' : areas,
'inst_areas' : inst_areas,
})
from numpy import median
filename = sys.argv[1]
col = int(sys.argv[2]) #number of columns
f = open(filename).read().split('\n')
#parse the equivalences file
sps = {}
for e in f:
if e == '' or e == '\t\t':
continue
else:
bline = e.split('\t')
sp = bline[0].split('_')[0]
sp = sp.split()
if 'SP.' in bline[0]:
sp = transform_sentence_case([sp[0]])[0]+' '+transform_lowercase([sp[1]])[0]
else:
sp = ' '.join(sp)#sp[0][0]+'. '+transform_lowercase([sp[1]])[0]
pdb=bline[1]
ind=bline[2]
if not sp in sps:
sps[sp]= []
sps[sp].append((pdb,ind))
else:
sps[sp].append((pdb,ind))
#create the table
t = open(filename[:filename.rfind('.')]+'.latextable','w')
header ='\\begin{table}[ht]\n\t\\tiny\n\t\\caption{}\n\t\\begin{center}\n\\begin{tabular}{ ccc'+' cc'*(col-1)
header += '}\n\t\\toprule\n\t Species'+ '& PDB & Plot'*col +'\\\\\n'
from numpy import median
filename = sys.argv[1]
col = int(sys.argv[2]) #number of columns
f = open(filename).read().split('\n')
#parse the equivalences file
sps = {}
for e in f:
if e == '' or e == '\t\t':
continue
else:
bline = e.split('\t')
sp = bline[0].split('_')[0]
sp = sp.split()
if 'SP.' in bline[0]:
sp = transform_sentence_case(
[sp[0]])[0] + ' ' + transform_lowercase([sp[1]])[0]
else:
sp = ' '.join(sp) #sp[0][0]+'. '+transform_lowercase([sp[1]])[0]
pdb = bline[1]
ind = bline[2]
if not sp in sps:
sps[sp] = []
sps[sp].append((pdb, ind))
else:
sps[sp].append((pdb, ind))
#create the table
t = open(filename[:filename.rfind('.')] + '.latextable', 'w')
header = '\\begin{table}[ht]\n\t\\tiny\n\t\\caption{}\n\t\\begin{center}\n\\begin{tabular}{ ccc' + ' cc' * (
col - 1)
