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
•
written
by
martinsindelar0077 •
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
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...
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