[Biopython] general scripting help

[Nat Echols]

Put all that code into a function with the file name or prefix as an
argument, then iterate over possible files:

def extract_alignments (prefix) :
  # old code goes here - append ".xml" to prefix to get alignment file name

for prefix in ["xaa","xab","xac"] :
  extract_alignments(prefix)

Or you could do this:

import os.path
for file_name in sys.argv[1:] :
  prefix = os.path.splitext(file_name)[0]
  extract_alignments(prefix)

And run as:

python my_script.py x*.xml

Assuming you have a real OS installed, of course - I'm not sure whether
Windows supports wildcards too.

-Nat



On Thu, Oct 10, 2013 at 3:36 PM, David Shin <davidsshin at lbl.gov> wrote:

> Hi -
>
> I am trying to write a script to parse through 50 or so deltablast .xml
> files.
>
> File names are:
> xaa.xml
> xab.xml
> xac.xml
> ...
>
>
> I'm new (2 days) to python, biopython, and just trying to have something to
> show for a meeting tomorrow. I have my script working well enough for one
> file, I was wondering if there was a way to go thru each file separately
> and output according to file name.
>
> ie. I'm trying to replace "xaa" in lines 3 and 12 with a wildcard like x??
> or even x*
>
>
> # This part gets the length of the query and stores to a variable
> from Bio import SeqIO
> record = SeqIO.read("xaa", "fasta")
> query_length = len(record)
> #print "query length:", query_length
>
> #This part gets the user's high and low percent identity cutoffs
> high_percent_cutoff = float(input("Enter high percent cutoff: "))
> low_percent_cutoff = float(input("Enter low percent cutoff: "))
>
> # This part does the comparison to all the hits if
> result_handle = open("xaa.xml")
> from Bio.Blast import NCBIXML
> blast_record = NCBIXML.read(result_handle)
>
> for alignment in blast_record.alignments:
>     for hsp in alignment.hsps:
>          alignment_length = alignment.length
>          identical_residues = hsp.identities
>          percent_identity = float(identical_residues) / float(query_length)
>          if alignment_length > query_length * 0.9 and alignment_length <
> query_length * 1.1 and percent_identity > low_percent_cutoff and
> percent_identity <= high_percent_cutoff:
>               print "****Alignment****"
>               print "sequence:", alignment.title
>               print "query length:", query_length
>               print "alighment length:", alignment.length
>               print "identical residues:", identical_residues
>               print "percent identity:", percent_identity
>               print
>               print
>
> "12345678901234567890123456789012345678901234567890123456789012345678901234567890"
>               print hsp.query[:80]
>               print hsp.match[:80]
>               print hsp.sbjct[:80]
>
>
> Thanks for any help.
> Dave
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