def display_message(self, msg, n_chars, punct, bgcol, txtcol):
buffer_out = pretty_output("REVERSE", bgcol, txtcol)
msg_out = pretty_output("REVERSE", "BOLD", bgcol)
half = (n_chars/2) + 1
if str(self.message_buffer)=='True' and str(self.message)=='True': # weird i have to specify ==True
buffer_out.write(punct.join([""] * half))
msg_out.write(msg)
buffer_out.write(punct.join([""] * half))
elif str(self.message)=='True' and str(self.message_buffer)=='False':
msg_out.write(msg)
elif str(self.message_buffer)=='True' and str(self.message)=='False':
buffer_out.write(punct.join([""] * half))
buffer_out.write(punct.join([""] * half))
def display(self, list_title):
try:
list = self.wunderlist.lists[list_title]
except KeyError:
print("That list does not exist.")
exit()
with colors.pretty_output(colors.BOLD, colors.UNDERSCORE) as out:
out.write(list_title)
for task_title, info in list["tasks"].iteritems():
pretty_print_task(task_title, info)
def overview(self):
for title, list in self.wunderlist.lists.iteritems():
tasks = list["tasks"]
with colors.pretty_output(colors.BOLD, colors.UNDERSCORE) as out:
out.write(title)
task_count = 0
for task_title, info in tasks.iteritems():
if task_count <= 4:
pretty_print_task(task_title, info)
task_count += 1
else:
break
print("")
def welcome(self):
with pretty_output("BOLD", "FG_MAGENTA") as start:
start.write(logo)
variPos = 1
elif vh == "H":
posRow = raw_input("In which row would you like to place your ship (Between 1 and " + str(size) + "): ")
posCol = raw_input(
"In which column would you like to place the left side your ship (Between 1 and " + str(size - 1) + "): "
)
clear()
while int(posRow) > size or int(posCol) > size - 1 or int(posCol) < 1 or int(posRow) < 1:
posRow = raw_input("In which row would you like to place your ship (Between 1 and " + str(size) + "): ")
posCol = raw_input(
"In which column would you like to place your ship (Between 1 and " + str(size - 1) + "): "
)
clear()
variPos = 1
else:
with colors.pretty_output(colors.BOLD, colors.FG_RED) as out:
out.write("You didn't type V or H!")
variPos = 0
ship_row = int(posRow) - 1
ship_col = int(posCol) - 1
if vh == "V":
pship_row = ship_row + 1
pship_col = ship_col
else:
pship_row = ship_row
pship_col = ship_col + 1
def guessCol(min, max):
return randint(min, max)
def printseq(samples, ref_seq, srange=[], width=100, htmlflag=False, dtype='tot'):
locus = {}
freqs = {}
seq = {}
if len(srange) == 1:
srange = [0,srange]
if len(srange) == 0:
srange = [0,len(ref_seq)]
out_name = 'Mito_SNP_%d_%d' % (srange[0], srange[1])
cseq = ''
if htmlflag:
cseq +='<html>\n<body>\n<pre>\n'
for sname in natsorted(samples.keys()):
sample = samples[sname]
sname = sname.rsplit('_',4)[0]
freqs1, locus1 = sample.mt.get_snps(min_freq, min_cov, dtype)
locus1 = locus1.flatten()
snps1 = sample.mt.snps[dtype][locus1,0]
seq1 = np.copy(ref_seq)
seq1[locus1] = snps1
locus.update({sname: locus1})
freqs.update({sname: freqs1})
seq.update({sname: seq1})
nline = int((srange[1]-srange[0])/width)
nends = (srange[1]-srange[0]) - width*nline
for i in range(nline):
cseq += ('%-10.10s' % '') + ('%-10d' % (srange[0]+i*width)) + (repr((srange[0]+(i+1)*width)).rjust(width-10)) + '\n'
for sname in natsorted(samples.keys()):
sname = sname.rsplit('_',4)[0]
locus1 = locus[sname] - srange[0] - i*width
freqs1 = freqs[sname]
seq1 = seq[sname][(srange[0]+i*width):(srange[0]+(i+1)*width)]
if htmlflag:
cseq += ('%-10.10s' % sname) + colorseqhtml(seq1, locus1, freqs1) + '\n'
else:
cseq += ('%-10.10s' % sname) + colorseq(seq1, locus1, freqs1) + '\n'
cseq += '....................\n'
if nends>0:
if nends>20:
cseq += ('%-10.10s' % '') + ('%-10d' % (srange[0]+nline*width)) + (repr(srange[1]).rjust(nends-10)) + '\n'
else:
cseq += ('%-10.10s' % '') + (repr(srange[1]).rjust(nends)) + '\n'
for sname in natsorted(samples.keys()):
sname = sname.rsplit('_',4)[0]
locus1 = locus[sname] - srange[0] - nline*width
freqs1 = freqs[sname]
seq1 = seq[sname][(srange[0]+nline*width):srange[1]]
if htmlflag:
cseq += ('%-10.10s' % sname) + colorseqhtml(seq1, locus1, freqs1) + '\n'
else:
cseq += ('%-10.10s' % sname) + colorseq(seq1, locus1, freqs1) + '\n'
if htmlflag:
cseq +='</pre>\n</body>\n</html>\n'
htmfile = open(save_dir+out_name+'.html', 'w')
htmfile.write(cseq)
htmfile.close()
#p1 = subprocess.Popen(['echo', cseq], stdout=subprocess.PIPE)
#p2 = subprocess.Popen(['aha > '+out_name+'.htm'], stdin=p1.stdout, stdout=subprocess.PIPE, shell=True)
#pdfkit.from_file(out_name+'.htm', out_name+'.pdf')
#print p2.communicate()
#subprocess.call(cmd)
else:
with clr.pretty_output() as out:
out.write(cseq)
