Hi Biostar,

I have two fasta files that I have blasted against one another and I am trying to make a list (dicitonary) of the top hits in a simple format of Query:Hit using Biopython. I am running into a an error, however, with the string's format. Here is an the script:

test_dictionary={}
blast_records = NCBIXML.parse(open(outfile))
for blast_record in blast_records:
    for alignment in blast_record.alignments:
        for hsp in alignment.hsps:
          test_dictionary.update({blast_record.query:alignment.title})

and here is an example dictionary entry where the u'' surrounds the value:

u'HA9WEQA08JTIW5': u'gnl|BL_ORD_ID|100 PhosphataseA'

however if I use the print command the values appear correct:

print alignment.title
gnl|BL_ORD_ID|100 PhosphataseA

I am sure this is a simple problem and results in my lack of understanding of precisely how Biopython stores its information. But any suggestions would be appreciated.

thanks zach cp

Edit *** as per DK's answer I ended up using this formulation where I split the output and keep the gene name:

 test_dictionary.update[str(blast_record.query)] = str(alignment.title).split()[1]