Re: Extracting lines from text files - script with a couple of 'side effects'
Hi, Thanks for the answers! And Dave, thanks for explaining the cause of the problem I will keep that in mind for the future. You're right, I am doing the search backward, it just seemed easier for me to do it in that way. Looks like I need to keep practising... Both your suggestions work, I will try and learn from them. Have a nice day Max -- https://mail.python.org/mailman/listinfo/python-list
Extracting lines from text files - script with a couple of 'side effects'
Dear All,
Here I am, with another newbie question. I am trying to extract some lines from
a fasta (text) file which match the headers in another file. i.e:
Fasta file:
header1|info1:info2_info3
general text
header2|info1:info2_info3
general text
headers file:
header1|info1:info2_info3
header2|info1:info2_info3
I want to create a third file, similar to the first one, but only containing
headers and text of what is listed in the second file. Also, I want to print
out how many headers were actually found from the second file to match the
first.
I have done a script which seems to work, but with a couple of 'side effects'
Here is my script:
---
import re
class Extractor():
def __init__(self,headers_file, fasta_file,output_file):
with open(headers_file,'r') as inp0:
counter0=0
container=''
inp0_bis=inp0.read().split('\n')
for x in inp0_bis:
container+=x.replace(':','_').replace('|','_')
with open(fasta_file,'r') as inp1:
inp1_bis=inp1.read().split('')
for i in inp1_bis:
i_bis= i.split('\n')
match =
re.search(i_bis[0].replace(':','_').replace('|','_'),container)
if match:
counter0+=1
with open(output_file,'at') as out0:
out0.write(''+i)
print '{} sequences were found'.format(counter0)
---
Side effects:
1) The very first header is written as header1 rather than header1
2) the number of sequences found is 1 more than the ones actually found!
Have you got any thoughts about causes/solutions?
Thanks for your time!
P.S.: I think I have removed the double posting... not sure...
Max
--
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Re: lstrip problem - beginner question
On Tuesday, June 4, 2013 11:21:53 AM UTC-4, mstagliamonte wrote:
Hi everyone,
I am a beginner in python and trying to find my way through... :)
I am writing a script to get numbers from the headers of a text file.
If the header is something like:
h01 = ('scaffold_1')
I just use:
h01.lstrip('scaffold_')
and this returns me with '1'
But, if the header is:
h02: ('contig-100_1')
if I use:
h02.lstrip('contig-100_')
this returns me with: ''
...basically nothing. What surprises me is that if I do in this other way:
h02b = h02.lstrip('contig-100')
I get h02b = ('_1')
and subsequently:
h02b.lstrip('_')
returns me with: '1' which is what I wanted!
Why is this happening? What am I missing?
Thanks for your help and attention
Max
--
http://mail.python.org/mailman/listinfo/python-list
lstrip problem - beginner question
Hi everyone,
I am a beginner in python and trying to find my way through... :)
I am writing a script to get numbers from the headers of a text file.
If the header is something like:
h01 = ('scaffold_1')
I just use:
h01.lstrip('scaffold_')
and this returns me '1'
But, if the header is:
h02: ('contig-100_0')
if I use:
h02.lstrip('contig-100_')
this returns me with: ''
...basically nothing. What surprises me is that if I do in this other way:
h02b = h02.lstrip('contig-100')
I get h02b = ('_1')
and subsequently:
h02b.lstrip('_')
returns me with: '1' which is what I wanted!
Why is this happening? What am I missing?
Thanks for your help and attention
Max
--
http://mail.python.org/mailman/listinfo/python-list
Re: lstrip problem - beginner question
On Tuesday, June 4, 2013 11:21:53 AM UTC-4, mstagliamonte wrote:
Hi everyone,
I am a beginner in python and trying to find my way through... :)
I am writing a script to get numbers from the headers of a text file.
If the header is something like:
h01 = ('scaffold_1')
I just use:
h01.lstrip('scaffold_')
and this returns me '1'
But, if the header is:
h02: ('contig-100_0')
if I use:
h02.lstrip('contig-100_')
this returns me with: ''
...basically nothing. What surprises me is that if I do in this other way:
h02b = h02.lstrip('contig-100')
I get h02b = ('_1')
and subsequently:
h02b.lstrip('_')
returns me with: '1' which is what I wanted!
Why is this happening? What am I missing?
Thanks for your help and attention
Max
edit: h02: ('contig-100_1')
--
http://mail.python.org/mailman/listinfo/python-list
Re: lstrip problem - beginner question
On Tuesday, June 4, 2013 11:21:53 AM UTC-4, mstagliamonte wrote:
Hi everyone,
I am a beginner in python and trying to find my way through... :)
I am writing a script to get numbers from the headers of a text file.
If the header is something like:
h01 = ('scaffold_1')
I just use:
h01.lstrip('scaffold_')
and this returns me '1'
But, if the header is:
h02: ('contig-100_0')
if I use:
h02.lstrip('contig-100_')
this returns me with: ''
...basically nothing. What surprises me is that if I do in this other way:
h02b = h02.lstrip('contig-100')
I get h02b = ('_1')
and subsequently:
h02b.lstrip('_')
returns me with: '1' which is what I wanted!
Why is this happening? What am I missing?
Thanks for your help and attention
Max
edit: h02= ('contig-100_1')
--
http://mail.python.org/mailman/listinfo/python-list
Re: lstrip problem - beginner question
On Tuesday, June 4, 2013 11:21:53 AM UTC-4, mstagliamonte wrote:
Hi everyone,
I am a beginner in python and trying to find my way through... :)
I am writing a script to get numbers from the headers of a text file.
If the header is something like:
h01 = ('scaffold_1')
I just use:
h01.lstrip('scaffold_')
and this returns me '1'
But, if the header is:
h02: ('contig-100_0')
if I use:
h02.lstrip('contig-100_')
this returns me with: ''
...basically nothing. What surprises me is that if I do in this other way:
h02b = h02.lstrip('contig-100')
I get h02b = ('_1')
and subsequently:
h02b.lstrip('_')
returns me with: '1' which is what I wanted!
Why is this happening? What am I missing?
Thanks for your help and attention
Max
edit:
h02= ('contig-100_1')
--
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Re: lstrip problem - beginner question
On Tuesday, June 4, 2013 11:41:43 AM UTC-4, Fábio Santos wrote:
On 4 Jun 2013 16:34, mstagliamonte madm...@yahoo.it wrote:
On Tuesday, June 4, 2013 11:21:53 AM UTC-4, mstagliamonte wrote:
Hi everyone,
I am a beginner in python and trying to find my way through... :)
I am writing a script to get numbers from the headers of a text file.
If the header is something like:
h01 = ('scaffold_1')
I just use:
h01.lstrip('scaffold_')
and this returns me '1'
But, if the header is:
h02: ('contig-100_0')
if I use:
h02.lstrip('contig-100_')
this returns me with: ''
...basically nothing. What surprises me is that if I do in this other way:
h02b = h02.lstrip('contig-100')
I get h02b = ('_1')
and subsequently:
h02b.lstrip('_')
returns me with: '1' which is what I wanted!
Why is this happening? What am I missing?
Thanks for your help and attention
Max
edit: h02: ('contig-100_1')
You don't have to use ('..') to declare a string. Just 'your string' will do.
You can use str.split to split your string by a character.
(Not tested)
string_on_left, numbers = 'contig-100_01'.split('-')
left_number, right_number = numbers.split('_')
left_number, right_number = int(left_number), int(right_number)
Of course, you will want to replace the variable names.
If you have more advanced parsing needs, you will want to look at regular
expressions or blobs.
Thanks, I will try it straight away. Still, I don't understand why the original
command is returning me with nothing !? Have you got any idea?
I am trying to understand a bit the 'nuts and bolts' of what I am doing and
this result does not make any sense to me
Regards
Max
--
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Re: lstrip problem - beginner question
On Tuesday, June 4, 2013 11:48:55 AM UTC-4, MRAB wrote:
On 04/06/2013 16:21, mstagliamonte wrote:
Hi everyone,
I am a beginner in python and trying to find my way through... :)
I am writing a script to get numbers from the headers of a text file.
If the header is something like:
h01 = ('scaffold_1')
I just use:
h01.lstrip('scaffold_')
and this returns me '1'
But, if the header is:
h02: ('contig-100_0')
if I use:
h02.lstrip('contig-100_')
this returns me with: ''
...basically nothing. What surprises me is that if I do in this other way:
h02b = h02.lstrip('contig-100')
I get h02b = ('_1')
and subsequently:
h02b.lstrip('_')
returns me with: '1' which is what I wanted!
Why is this happening? What am I missing?
The methods 'lstrip', 'rstrip' and 'strip' don't strip a string, they
strip characters.
You should think of the argument as a set of characters to be removed.
This code:
h01.lstrip('scaffold_')
will return the result of stripping the characters '', '_', 'a', 'c',
'd', 'f', 'l', 'o' and 's' from the left-hand end of h01.
A simpler example:
'xyyxyabc'.lstrip('xy')
'abc'
It strips the characters 'x' and 'y' from the string, not the string
'xy' as such.
They are that way because they have been in Python for a long time,
long before sets and such like were added to the language.
Hey,
Great! Now I understand!
So, basically, it is also stripping the numbers after the '_' !!
Thank you, I know a bit more now!
Have a nice day everyone :)
Max
--
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Re: lstrip problem - beginner question
Thanks to everyone! I didn't expect so many replies in such a short time! Regards, Max -- http://mail.python.org/mailman/listinfo/python-list
