Python Program Accepting Fasta And Blast, Outputting In Xml Then Returning Ids Of All Sequences

Question

[te502]

Ok. The assignment was to write a program which accepts an input argument of a FASTA file and prints the hit_id of all found sequences using three functions: run_blast (accepting the FASTA and optional input for BLAST, then using subprocess executes BLAST with BLAST output in XML format), read_blast (accepts the above BLAST XML file and returns IDs of sequences), and main (contains main processes the script will execute).

After 4 hours, all I can come up with is this:

import subprocess
from Bio.Blast import NCBIXML
def run_blast(fasta_filename,blastoutput):
    f=open(fasta_filename,'r')###opening the file with reading access           
    lines=f.read() ###lines equates to reading                                  
    col=lines.split("\n")###splits first and second lines                       
    sequence=col[1] ###gives this second column a name                          
    return sequence ###returns the answer of the second line of the FASTA       
fasta_filename='RBP1a.fa'###defining file names                                 
blastoutput='RBP1a.xml'
subprocess.call(['blastn','-query',"fasta_filename",'-db','nt','-outfmt','5','-\
out','blastoutput']) ###blast output in xml form                                
from Bio.Blast import NCBIXML
record=NCBIXML.read(open("blastoutput"))

def read_blast(blastoutput):

#####I don't even know what to put in order to extract the sequences from the XML file. Something about the order isn't correct here.

[Asaf]

I suggest you take a look at the cookbook http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc86 There is an example of a similar thing, I can send you a code that does that if you'd like.

[te502]

I've been trying to go off of the cookbook, but I don't see where it uses subprocess (which is required in our assignment). I'm a Master's student in BIOLOGY. It was quite a mistake to take this class with no prior programming knowledge.

[Peter]

The Biopython application wrappers can do the subprocess bit for you, but but some of the more advanced examples using stdin/stdout elsewhere in the Biopython Tutorial do this explicitly.

[te502]

but I would absolutely appreciate it if you could it to me! :)

[Peter]

BioStars isn't really intended for helping people to cheat on their coursework - if you want to share an example, post it openly here please.