Hi group, I am trying to substitute in the following way and i cannot. Could
you point out whats wrong in what i am doing.
>>> z'.|D'
>>> re.sub(z,'1',z)'111'
I just want only '1' and not '111'.
I want:>>> re.sub(z,'1',z)'1'
re.sub is repeatedly inserting 3 times because z has .|D . How can I
Hi :
I have some strings with both alpha-numeric strings. I want to add all the
numbers in that string and leave characters and special characters.
1A0G19
5G0C25^C52
0G2T3T91
44^C70
How can I count only the numbers in the above.
1 A 0 G 19 = 1+0+19 = 20
5 G 0 C 25 ^C 52 =
Hi group:
I have a list:
k = ['T', 'C', 'T', 'T', 'T', 'T', 'T', 'T', 'T', 'C', 'T', 'T', 'T', 'C',
'T',
'T', 'T', 'C', 'C', 'T', 'T', 'T', 'C', 'T', 'T', 'T', 'T', 'T', 'T']
the allowed elements are A or T or G or C. List can have any number of A or T
or
G or C
My aim is to get a string
Dear group:
I need some tips/help from experts.
I have two files tab-delimted.
One file is 4K lines. The other files is 40K lines.
I want to search contents of a file to other and print those lines that satisfy.
File 1:
chr X Y
chr18337733 8337767
Dear group:
I have a large file 3GB. Each line is a tab delim file.
example lines of it:
585 chr1433 433 rs56289060 0 + - -
-/C genomic insertion unknown 0 0 unknown between 1
585 chr1491 492 rs55998931 0
= raw_input()
EOFError: EOF when reading a line
How to notify that at EOF break and suppress exception.
thanks
- Original Message
From: kumar s ps_pyt...@yahoo.com
To: tutor@python.org
Sent: Mon, March 15, 2010 6:52:26 PM
Subject: [Tutor] raw_input()
Dear group:
I have a large file
thanks Benno.
supplying 3.6 GB file is over-kill for the script. This is the reason I chose
to input lines on fly.
thanks
Kumar
- Original Message
From: Benno Lang transmogribe...@gmail.com
To: kumar s ps_pyt...@yahoo.com
Cc: tutor@python.org
Sent: Mon, March 15, 2010 7:19:24
dear tutors:
I have two files. I want to take coordiates of an row in fileA and find if they
are in the range of coordinates in fileB. If they are, I want to be able to map
else, pass.
thanks
kumar
file a:
name loc x y
a 4 4081159640811620
b 4
Dear group,
unfortunately my previous post got tagged as
'homework' mail and got no responses.
In short, I have a dictionary structure as depicted
below.
I want to go over every key and print the key,value
pairs in a more sensible way.
I have written a small piece of code. May I request
hi group,
i have a data obtained from other student(over 100K)
lines that looks like this:
(39577484, 39577692) [['NM_003750']]
(107906, 108011) [['NM_002443']]
(113426, 113750) [['NM_138634', 'NM_002443']]
(106886, 106991) [['NM_138634', 'NM_002443']]
(100708, 100742) [['NM_138634',
correctly in
terms of exons, transcripts. If not I would be happy
to send you a pdf file with a figure.
Thanks again.
--- Danny Yoo [EMAIL PROTECTED] wrote:
On Mon, 16 Oct 2006, kumar s wrote:
I have a simple question to ask tutors:
list A :
a = [10,15,18,20,25,30,40]
Hi Kumar
In continuation to :
Re: [Tutor] extracting numbers from a list
hello list
I have coordinates for exons (chunks of sequence). For
instance:
10 - 50 A
10 - 20 B
35 - 50 B
60 - 70 A
60 - 70 B
80 - 100 A
80 - 100 B
(The above coordinates and names are easier than in
dat)
Here my aim is to
hi :
I have a simple question to ask tutors:
list A :
a = [10,15,18,20,25,30,40]
I want to print
10 15 (first two elements)
16 18 (16 is last number +1)
19 20
21 25
26 30
31 40
fx = a[0]
fy = a[1]
b = a[2:]
ai = iter(b)
last = ai.next()
for j in ai:
... print fy+1,last
... last
hi,
the reason could be that I did not quite understand
the concept of looping
I have a list of 48 elements
I want to create another two lists , listA and listB
I want to loop through the list with 48 elements and
select element with index 0,3,6,9,12 ..etc into listA
select elements with
PROTECTED] wrote:
keep a counter in your loop. is this a homework
question?
On Sep 23, 2006, at 8:34 AM, kumar s wrote:
hi,
the reason could be that I did not quite
understand
the concept of looping
I have a list of 48 elements
I want to create another two lists , listA
Hi Danny:
I have ~50 files in this format:
File1:
680:209 3006.3
266:123 250.5
62:393 117.3
547:429 161.5
341:311 546.5
132:419 163.3
98:471 306.3
File 2:
266:123 168.0
62:393 119.3
547:429 131.0
341:311 162.3
132:419 149.5
98:471 85.0
289:215 207.0
75:553 517.0
I am generating these
Hi Kent,
Thank you for your suggestion. I keep getting
IOError permission denied every time I try the tips
that you provided. I tried to lookup on this error and
did not get reasonable answer. Is this error something
to do with Windows OS?
Any suggestions.
Thank you
K
allColumns =
Hello.
I wrote a parser to parse spot intensities. The input
to this parser i am giving one single file
f1 = open('my_intensity_file.dml','r')
int = f1.read().split('\n')
my_vals = intParser(int)
intParser return a list
f2 = open('myvalues.txt','w')
for line in my_vals:
f2.write(line)
if you typed ls
*.dml or whatever into a
command prompt. There wasn't too much info about
specifically how you needed
this to work, so this is a rough sketch of what you
want. Hopefully it helps.
-Jay
On Sunday 30 January 2005 03:03 am, kumar s wrote:
Hello.
I wrote a parser
nmr = nmrows[i]
pbr = cols[0]
print nmrow[i] +'\t'+cols[0]
nmr = str(nmrows[i])
pbr = cols[0]
print nmrow[i]+'\t'+cols[0]
will print what you want.
k
--- Srinivas Iyyer [EMAIL PROTECTED] wrote:
Hello group,
I am trying to print rows from two lists together:
how can i deal with
Hello:
In append function instead of appending one below the
other can I append one next to other.
I have a bunch of files where the first column is
always the same. I want to collect all those files,
extract the second columns by file wise and write the
first column, followed by the other
Hi:
I am still trying to learn the OOPs side of python.
however, things/circumstances dont seems to stop until
I finish my practise and attaing higher understanding.
may be, i am being pushed by circumstances into the
stream and i am being tested if I can swim efficiently
while I struggle with
Dear group:
I have two lists:
1. Lseq:
len(Lseq)
30673
Lseq[20:25]
['NM_025164', 'NM_025164', 'NM_012384', 'NM_006380',
'NM_007032','NM_014332']
2. refseq:
len(refseq)
1080945
refseq[0:25]
['gi|10047089|ref|NM_014332.1| Homo sapiens small
muscle protein, X-linked (SMPX), mRNA',
+'\t'+cols[1]+'\t'+cols[2])
--- Danny Yoo [EMAIL PROTECTED] wrote:
On Fri, 14 Jan 2005, kumar s wrote:
for i in range(len(what)):
ele = split(what[i],'\t')
cor1 = ele[0]
for k in range(len(my_report)):
cols = split(my_report[k],'\t')
cor
[index]='
Try that.
Argh, my head. You do some strange things to
Python.
Liam Clarke
On Thu, 13 Jan 2005 10:56:00 -0800 (PST), kumar s
[EMAIL PROTECTED] wrote:
Dear group:
My list looks like this: List name = probe_pairs
Name=AFFX-BioB-5_at
Cell1=96369 N
Dear group,
I am frustrated to ask some questions on topics that I
thought covered well. my logic is not correct.
I have a simple list:
a
['a', 'apple', 'b', 'boy', 'c', 'cat']
I want to create a dictionary:
dict = {'a':'apple',
'b':'boy',
'c':'cat'}
my way of doing this
Dear group,
For some reason my brain cannot think of any other
option than what I have in my script. Could any one
please help me in suggesting.
What I have : (File name : psl)
22 2 457:411 25 0
25 0 457:411 25 0
25 0 457:411 25 0
25 0
0
25 0 624:69 25 0
25 0 350:239 25 0
Is this a correct approach?
Thanks
K.
--- kumar s [EMAIL PROTECTED] wrote:
Dear group,
For some reason my brain cannot think of any other
option than what I have in my script. Could any one
please help me
Dear group,
I have written a small piece of code that takes a file
and selects the columns that I am interested in and
checks the value of the column on a condition (value
that eqauls 25) and then write it the to another file.
Code:
import sys
from string import split
import string
print enter
Dear group:
I am trying to parse BLAST output (Basic Local
Alignment Search Tool, size around more than 250 KB
).
- Hit
Hit_num1/Hit_num
Hit_idgi|43442325|emb|BX956931.1|/Hit_id
Hit_defDKFZp781D1095_r1 781 (synonym: hlcc4) Homo
sapiens cDNA clone DKFZp781D1095 5', mRNA
sequence./Hit_def
PROTECTED] wrote:
On Fri, 31 Dec 2004, kumar s wrote:
I am trying to parse BLAST output (Basic Local
Alignment Search Tool,
size around more than 250 KB ).
[xml text cut]
Hi Kumar,
Just as a side note: have you looked at Biopython
yet?
http://biopython.org/
I
Hi Group:
I have Question:
How can I substitute an object as a pattern in making
a pattern.
x = 30
pattern = re.compile(x)
My situation:
I have a list of numbers that I have to match in
another list and write them to a new file:
List 1: range_cors
range_cors[1:5]
['161:378', '334:3',
30, Married, will soon be a dad., Live in Baltimore,
U.S.A. and I am a Ph.D. student
I lived in Denmark and Israel in the past as a part
of my research life.
Will finish my Ph.D., in Bioinformatics.
Got introduced to computers at the age of 25 :-(
and more happy it is not 52 :-)
Programming
Thank you for clearing up some mist here. In fact I
was depressed by that e-mail because there are not
many tutorials that clearly explains the issues that
one faces while trying to code in python. Also, due
to lack of people who are proficient in python around
our univ. campus in baltimore, i
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