I'm trying to isolate, from a bam file, those sequencing reads that have insertions longer than number (let's say 50bp). I guess I can do that using the cigar but I don't know any easy way to parse it and keep only the reads that I want. This is what I need:
Read1 -> 2M1I89M53I2M
Read2 -> 2M1I144M
I should keep only Read1.
Thanks!
Most likely I'm late, but ...
Probably you want MC tag, not CIGAR. I use BWA, and information on insertions is stored in the MC tag. But I may mistake.
Use pysam module to parse BAM, and regular expressions to parse MC tags.
Example code:
import pysam
import re
input_file = pysam.AlignmentFile('input.bam', 'rb')
output_file = pysam.AlignmentFile('found.bam', 'wb', template = input_file)
for Read in input_file:
try:
TagMC = Read.get_tag('MC')
except KeyError:
continue
InsertionsTags = re.findall('\d+I', TagMC)
if not InsertionsTags: continue
InsertionLengths = [int(Item[:-1]) for Item in InsertionsTags]
MinLength = min(InsertionLengths)
if MinLength > 50: output_file.write(Read)
input_file.close()
output_file.close()
Hope that helps.
I get the following lxml.etree.XPathEvalError: Invalid predicate error:
Traceback (most recent call last):
File "check_1337.py", line 18, in
//div[#class = "_3iyw"]//div[#class = "_6beq _7cdk _6beo"]//div[#class = "_7om2 _3gim _ 7cdk"]//div [#class = "5s61"]//div[#class = "_7cdi"]')
File "src\lxml\etree.pyx", line 1583, in lxml.etree._Element.xpath
File "src\lxml\xpath.pxi", line 305, in lxml.etree.XPathElementEvaluator.call
File "src\lxml\xpath.pxi", line 225, in lxml.etree._XPathEvaluatorBase._handle_result
lxml.etree.XPathEvalError: Invalid predicate
from the following code:
from lxml.etree import HTML
import requests
url = "https://m.facebook.com/?_rdr"
response = requests.get(url)
root = HTML(response.content)
tempII = root.find("body").xpath('//div[#id = "viewport"]//div[#id = "page"]//div[#id = "rootcontainer]//div[#class = "async_compose _2v9s"]//div[#id = "MRoot"]\
//div[#class = "_3iyw"]//div[#class = "_6beq _7cdk _6beo"]//div[#class = "_7om2 _3gim _ 7cdk"]//div [#class = "5s61"]//div[#class = "_7cdi"]')
print (tempII)
Can you help me find out the reason for this error?
Take a look at rootcontainer in your find call.
Before this word you put a double quote (this is OK),
but failed to put another double quote after it.
Another detail: A bit later you have: #class = "_7om2 _3gim _ 7cdk".
Are you sure that there should be four classes here (_7om2, _3gim,
_ and 7cdk)?
Using "_" as a class name is a weird practice.
Maybe instead of 2 last classes there should be one class _7cdk?
Note that a bit earlier you have just _7cdk.
This flaw is not likely to cause any exception, but the result of find
probably will be empty.
Be cautious as you write such predicates, as errors like this are quite
difficult to identify.
So I made this very small function. it is a bonehead easy function but frankly borderline my capabilities.. Im learning. The function works as expected, but I would like to go further. I would like to make it so I can either give it an argument (a username) and just get the information for that single user, or default to reporting all users. is this possible w/o starting over from what I have so far?
I have just poked around and seen some examples but nothing that I can fit into my script. that I can understand at least.
import boto3
iam = boto3.client('iam')
def user_group():
for myusers in iam.list_users()['Users']:
Group = iam.list_groups_for_user(UserName=myusers['UserName'])
print("User: " + myusers['UserName'])
for groupName in Group['Groups']:
print("Group: " + groupName['GroupName'])
print("----------------------------")
user_group()
I would like to have the ability to run this script in two fashions.
1) add an argument(s) of 'username' so I can get the response for a particular user
2) default to getting response for all users if no argument is given.
This can be done by using an argument with a default value:
def user_group(user = None):
if user is None:
print("No user")
else:
print(user)
user_group()
user_group('some user')
prints
No user
some user
In your case you may want to write
def user_group(user = None):
users_to_list = iam.list_users()['Users'] if user is None else [user]
for myusers in user_to_list:
...
Here is the code I have for reading a text file a storing it as a dictionary:
from sys import argv
def data(file):
d = {}
for line in file:
if line.strip() != '':
key,value = line.split(":")
if key == 'RootObject':
continue
if key == 'Object':
obj = value.strip()
d[obj]={}
else:
d[obj][key] = value.strip()
return d
file = open(argv[1])
planets = data(file)
print(planets)
My question is did I implement the argv correctly so that any user can run the dictionary by just typing solardictionary.py random.txt in the commandline and run it. I tried running this but I keep getting an index error and I'm not sure there might be something wrong with my argv implementation.
You need to type file = open(sys.argv[1],'r') in order to access the array because it is contained within the sys module.
http://docs.python.org/3.1/library/sys.html#module-sys
You may also be interested in opening the file within a try-catch block.
I am trying to select data from a table in SQLite one row ONLY at a time for each call to the function, and I want the row to increment on each call (self.count is initialized elsewhere and 'line' is irrelevant here) I am using an adbapi connection pool in Twisted to connect to the DB. Here is the code I have tried:
def queryBTData4(self,line):
self.count=self.count+1
uuId=self.count
query="SELECT co2_data, patient_Id FROM btdata4 WHERE uid=:uid",{"uid": uuId}
d = self.dbpool.runQuery(query)
return d
This code works if I just set uid=1 or any other number in the DB (I used autoincrement for uid when I created the DB) but when I try to assign a value to uid (i.e. self.count via uuId) it reports that the operator has to be string or unicode.(I have tried both but it does not seem to help) However, I know that the query statement above works just fine in a previous program when I use a cursor and the execute command but I cannot see why it does not work here. I have tried all sorts of combinations and searched for a solution but have not found anything yet that works.(I have also tried the statement with brackets and other forms)
Thanks for any help or advice.
Here is the entire code:
from twisted.internet import protocol, reactor
from twisted.protocols import basic
from twisted.enterprise import adbapi
import sqlite3, time
class ServerProtocol(basic.LineReceiver):
def __init__(self):
self.conn = sqlite3.connect('biomed2.db',check_same_thread=False)
self.dbpool = adbapi.ConnectionPool("sqlite3" , 'biomed2.db', check_same_thread=False)
def connectionMade(self):
self.sendLine("conn made")
factory = protocol.ClientFactory()
factory.protocol = ClientProtocol
factory.originator = self
reactor.connectTCP('localhost', 1234, factory)
def lineReceived(self, line):
self._received = line
self.insertBTData4(self._received)
self.sendLine("line recvd")
def forwardLine(self, recipient):
recipient.sendLine(self._received)
def insertBTData4(self,data):
print "data in insert is",data
chx=data
PID=2
device_ID=5
query="INSERT INTO btdata4(co2_data,patient_Id, sensor_Id) VALUES ('%s','%s','%s')" % (chx, PID, device_ID)
dF = self.dbpool.runQuery(query)
return dF
class ClientProtocol(basic.LineReceiver):
def __init__(self):
self.conn = sqlite3.connect('biomed2.db',check_same_thread=False)
self.dbpool = adbapi.ConnectionPool("sqlite3" , 'biomed2.db', check_same_thread=False)
self.count=0
def connectionMade(self):
print "server-client made connection with client"
self.factory.originator.forwardLine(self)
#self.transport.loseConnection()
def lineReceived(self, line):
d=self.queryBTData4(self)
d.addCallbacks(self.sendData,self.printError )
def queryBTData4(self,line):
self.count=self.count+1
query=("SELECT co2_data, patient_Id FROM btdata4 WHERE uid=:uid",{"uid": uuId})
dF = self.dbpool.runQuery(query)
return dF
def sendData(self,line):
data=str(line)
self.sendLine(data)
def printError(self,error):
print "Got Error: %r" % error
error.printTraceback()
def main():
factory = protocol.ServerFactory()
factory.protocol = ServerProtocol
reactor.listenTCP(4321, factory)
reactor.run()
if __name__ == '__main__':
main()
The DB is created in another program, thus:
import sqlite3, time, string
conn = sqlite3.connect('biomed2.db')
c = conn.cursor()
c.execute('''CREATE TABLE btdata4
(uid INTEGER PRIMARY KEY, co2_data integer, patient_Id integer, sensor_Id integer)''')
The main program takes data into the server socket and inserts into DB. On the client socket side, data is removed from the DB one line at a time and sent to an external server. The program also has the ability to send data from the server side to the client side if required but I am not doing so here at the moment.
In queryBTData(), every time the function is called the count increments and I assign that value to uuId, which I then pass to the query. I have had this query statement working in a program where I do not use the adbapi but it does not seem to work here. I hope this is clear enough but if not please let me know and I will try again.
EDIT:
I have modified the program to take one row from the DB at a time (see queryBTData() below) but have come across another problem.
def queryBTData4(self,line):
self.count=self.count+1
xuId= self.count
#xuId=10
return self.dbpool.runQuery("SELECT co2_data FROM btdata4 WHERE uid = ?",xuId)
#return self.dbpool.runQuery("SELECT co2_data FROM btdata4 WHERE uid = 10")
When the count gets to 10 I get an error (which I will post below) which states that: "Incorrect number of bindings supplied. The current statement uses 1, and there are 2 supplied"
I have tried setting xuId to 10 (see commented out line xuId=10) but I still get the same error. However, if I switch the return statements (to commented out return) I do indeed get correct row with no error. I have tried converting xuId to unicode but that makes no difference, I still get the same error. Basically, if I I set uid in the return statement to 10 or more (commented out return) it works, but if I set uid to xuId (i.e. uid=?,xuId) in the first return, it only works when xuId is below 10. The API documentation, as far as I can tell, gives no clue as to why this occurs.(I have also disabled the insert into DB to eliminate this and checked the SQLite3_ limit, which is 999)
Here are the errors I am getting when using the first return statement.
Got Error: <twisted.python.failure.Failure <class 'sqlite3.ProgrammingError'>>
Traceback (most recent call last):
File "c:\python26\lib\threading.py", line 504, in __bootstrap
self.__bootstrap_inner()
File "c:\python26\lib\threading.py", line 532, in __bootstrap_inner
self.run()
File "c:\python26\lib\threading.py", line 484, in run
self.__target(*self.__args, **self.__kwargs)
--- <exception caught here> ---
File "c:\python26\lib\site-packages\twisted\python\threadpool.py", line 207, i
n _worker
result = context.call(ctx, function, *args, **kwargs)
File "c:\python26\lib\site-packages\twisted\python\context.py", line 118, in c
allWithContext
return self.currentContext().callWithContext(ctx, func, *args, **kw)
File "c:\python26\lib\site-packages\twisted\python\context.py", line 81, in ca
llWithContext
return func(*args,**kw)
File "c:\python26\lib\site-packages\twisted\enterprise\adbapi.py", line 448, i
n _runInteraction
result = interaction(trans, *args, **kw)
File "c:\python26\lib\site-packages\twisted\enterprise\adbapi.py", line 462, i
n _runQuery
trans.execute(*args, **kw)
sqlite3.ProgrammingError: Incorrect number of bindings supplied. The current sta
tement uses 1, and there are 2 supplied.
Thanks.
Consider the API documentation for runQuery. Next, consider the difference between these three function calls:
c = a, b
f(a, b)
f((a, b))
f(c)
Finally, don't paraphrase error messages. Always quote them verbatim. Copy/paste whenever possible; make a note when you've manually transcribed them.