async def on_message(message):
# Ignore bots completely (including ourself)
if message.author.bot:
return
if dbg.should_ignore_message(message):
return
try:
# Check if we need to congratulate a user on getting a new role
lvl_up_message = await tr.user_speaks(message.author)
if lvl_up_message != None:
await message.channel.send(lvl_up_message)
# Check if someone is trying to use a bot command
if message.content != "" and message.content[0] == CMD_PREFIX:
prefix_removed = utils.strip_prefix(message.content)
if prefix_removed == "":
return
command = utils.get_command(prefix_removed)
if command in FUNC_DICT:
# First, check if they're using a built-in command
output_message = await FUNC_DICT[command](message)
if output_message != None:
await message.channel.send(output_message)
elif cc.command_available(command):
# Check if they're using a user-defined command
cmd_output = cc.parse_response(message)
await message.channel.send(cmd_output)
except discord.errors.HTTPException as e:
print("HTTPException: {}".format(str(e)))
pass
def parse_input(input):
rule_segment, my_ticket_segment, other_ticket_segment = input.split('\n\n')
rules = {
name: values
for name, values in (parse_rule(rule)
for rule in rule_segment.splitlines())
}
my_ticket = [
int(s)
for s in strip_prefix(my_ticket_segment, 'your ticket:\n').split(',')
]
print(my_ticket)
other_tickets = [
[int(s) for s in line.split(',')] for line in strip_prefix(
other_ticket_segment, 'nearby tickets:\n').splitlines()
]
return rules, my_ticket, other_tickets
def parse_response(self, message):
prefix_removed = utils.strip_prefix(message.content)
command = utils.get_command(prefix_removed)
response = self.cmd_dict[command]
# Check if they want to embed a ping within the response
mentioned_id = parse_mention(message)
if mentioned_id != None:
ping = "<@!{}>".format(mentioned_id)
else:
ping = ""
response = response.replace("%mention%", ping)
return response
async def on_message(message):
# Do not react to our own messages
if message.author.id == client.user.id:
return
try:
# Check if someone is using a bot command
if message.content != "" and message.content[0] == CMD_PREFIX:
prefix_removed = utils.strip_prefix(message.content)
if prefix_removed == "":
return
command = utils.get_command(prefix_removed)
if command in FUNC_DICT:
output = await FUNC_DICT[command](message)
if output != None:
await message.channel.send(output)
except Exception as e:
print(traceback.format_exc())
async def on_message(message):
# Ignore bots completely (including ourself)
if message.author.bot:
return
# Check first if we're toggling debug mode
# Need to do this before we discard a message
if dbg.check_toggle(message):
await dbg.toggle_debug(message)
return
elif dbg.should_ignore_message(message):
return
try:
# Keep track of the user's message for dynamic slowmode
await thermo.user_spoke(message)
# Check if we need to congratulate a user on getting a new role
# Don't award XP if posting in specified disabled channels
if message.channel.id not in XP_OFF:
lvl_up_message = await tr.give_xp(message.author)
if lvl_up_message != None:
await message.channel.send(lvl_up_message)
# Check if someone is trying to use a bot command
if message.content != "" and message.content[0] == CMD_PREFIX:
prefix_removed = utils.strip_prefix(message.content)
if prefix_removed == "":
return
command = utils.get_command(prefix_removed)
if command in FUNC_DICT:
# First, check if they're using a built-in command
output_message = await FUNC_DICT[command](message)
if output_message != None:
await message.channel.send(output_message)
elif cc.command_available(command):
# Check if they're using a user-defined command
cmd_output = cc.parse_response(message)
await message.channel.send(cmd_output)
except discord.errors.HTTPException as e:
print(f"HTTPException: {str(e)}")
pass
def check_toggle(self, message):
prefix_removed = strip_prefix(message.content)
if prefix_removed == "" or message.content[0] != CMD_PREFIX:
return False
command = get_command(prefix_removed)
return command == "debug"
gene_metadata = pd.read_table(lbs_dir / 'mutLBSgene_basic.txt')
lbs_muts = pd.read_table(lbs_dir /
'mutLBSgene_tcga_cosmic_overlapped_mutations.txt')
lbs_genes = sorted(set(lbs_muts.gene))
missing_from_tcga = set(lbs_genes) - set(genes)
print('Genes in LBS data but not TCGA mutation data:', len(missing_from_tcga))
lbs_mut_set = set(zip(lbs_muts.gene, lbs_muts.nsSNV))
# set of tuples of (patient, gene, AA sub)
brca_muts_in_lbs = set()
for i, row in muts.iterrows():
if isinstance(row.HGVSp_Short, float):
# null
continue
aa_sub = strip_prefix(row.HGVSp_Short, 'p.')
patient = get_patient_barcode(row.Tumor_Sample_Barcode)
gene = row.Hugo_Symbol
if (gene, aa_sub) in lbs_mut_set:
item = (patient, gene, aa_sub)
brca_muts_in_lbs.add(item)
print('Found LBS mut:', item)
data_path = create_data_path('intersect_muts_lbs')
lbs_mut_df = pd.DataFrame(list(brca_muts_in_lbs))
lbs_mut_df.columns = ['patient', 'gene', 'aa_sub']
tcga_mut_path = data_path / 'brca_lbs_muts.csv'
print('Saving BRCA mutations in LBS DB to', tcga_mut_path)
lbs_mut_df.to_csv(tcga_mut_path, index=None)