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To: python-list@python.org
From: Dave Angel <davea@davea.name>
Subject: Re: Extracting lines from text files - script with a couple of 'side effects'
Date: Wed, 25 Sep 2013 21:02:07 +0000 (UTC)
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On 25/9/2013 16:06, mstagliamonte wrote:

> 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?
>

The cause is the same.  The first line in the file starts with a "<",
and you're splitting on the same.  So the first item of inp1_bis is the
empty string.  That string is certainly contained within container, so
it matches, and produces a result of ">"

You can "fix" this by adding a line after the "for i in inp1_bis" line
    if not i: continue

But it also seems to me you're doing the search backwards.  if the Fasta
file has a line like: >der

it would be considered a match!  Seems to me you'd want to only match
lines which contain an entire header.


-- 
DaveA