How to get organism description from BLAST output using biopython

Question

[martinsindelar0077]

Hello, I woud like to ask you... I have file of like 1000 sequences from BLAST results with clasic header like this...

">PLN78092.1 putative endo-1,3(4)-beta-glucanase [Aspergillus taichungensis]"

I would like to change the header of every sequence to contain only name of organisms... using biopython.

">Aspergillus taichungensis"

When I download results in fasta format and I parse it using biopython I can find organism name only in description, but in desctiption there is a whole header

from Bio import SeqIO

records = list(SeqIO.parse("sequence.fasta", "fasta"))

for x in range (len(records)):

print(records[x].description)

PLN78092.1 putative endo-1,3(4)-beta-glucanase [Aspergillus taichungensis] ...

Ofcourse I could just extract text in brackets "[ ]", but is there any way how to get only the name for example by parsing .xml format of results? Something like this:

from Bio.Blast import NCBIXML

result_handle = open("sequences.xml")

blast_records = NCBIXML.parse(result_handle)

blast_records = list(blast_records)

print(blast_records[0].organism) #this is not working

[GenoMax]

Please use the formatting bar (especially the code option) to present your post better.

Thank you!

Answer 1

[massa.kassa.sc3na]

Hi, this is done as follows:

result_handle = open("sequences.xml", 'r')
blast_records = list(NCBIXML.parse(result_handle))
one_query = blast_records[0]            # one blast query
one_hit = one_query.alignments[0]       # this is one hit
print(one_hit.hit_def)                  # this is probably what you want
print(one_hit.hit_id)                   # you might also want this

[martinsindelar0077]

Thank you! Actually this didn't solved my problem, but now I see where is problem... BLAST output has no attribute describing only organism... in hit_def there is again whole description ... so I'll just extract text in brackets...