retrieve sequence alignment score produced by emboss in biopython
Question: I'm trying to retrieve the alignment score of two sequences compared using
emboss in biopython. The only way that I know is to retrieve it from an output
text file produced by emboss. The problem is that there will be hundreds of
these files to iterate over. Is there an easier/cleaner method to retrieve the
alignment score, without resorting to that? This is the main part of the code
that I'm using.

    
    
    From Bio.Emboss.Applications import StretcherCommandline
    needle_cline = StretcherCommandline(asequence=,bsequence=,gapopen=,gapextend=,outfile=)
    stdout, stderr = needle_cline()
    


Answer: I had the same problem and after some time spent on searching for a neat
solution I popped up a white flag.

However, to speed up significantly the processing of output files I did the
following things:

1) I used _re_ python module for handling regular expressions to extract all
data needed.  

2) I created a ramdisk space for the output files. The use of a ramdisk here
allowed for processing and exchanging all the data in RAM memory (much faster
than writing and reading the output files from a hard drive, not to mention it
saves your hdd in case of processing massive number of alignments).

