Extracting lines from text files - script with a couple of 'side effects'

[mstagliamonte]

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