[BioPython] How can I get a more explicite error
Yvan.Strahm at bccs.uib.no
Yvan.Strahm at bccs.uib.no
Wed Mar 18 18:47:58 UTC 2009
Hello List,
I try to get a grip on Biopython and followed the chapter 6 form the
tutorial (http://www.biopython.org/DIST/docs/tutorial/Tutorial.html)
I run this script:
from Bio.Blast import NCBIStandalone
import re
import sys
my_blast_db =
"/export/scratch/yvans/BEE/Apis_mellifera_ligustica_complete_mitochondrial_genome.fasta"
my_blast_file = sys.argv[1]
my_blast_exe = "/Home/lundalm/yvans/src/blast-2.2.19/bin/blastall"
result_handle, error_handle = NCBIStandalone.blastall(my_blast_exe, "blastn",
my_blast_db,
my_blast_file,
gap_open=5,
gap_extend=2,
filter ='F',
expectation=1000)
blast_results = result_handle.read()
my_results=sys.argv[1]+".xml"
save_file = open(my_results, "w")
save_file.write(blast_results)
save_file.close()
I got this error
[yvans at lundalm BEE]$ python bioblast.py s_1_2_eland_extended.8000000.fta
Traceback (most recent call last):
File "bioblast.py", line 16, in <module>
blast_results = result_handle.read()
SystemError: Objects/stringobject.c:4271: bad argument to internal function
if the number of sequence blasted agianst the db is greater than 500000.
The sequence are small reads from a solexa sequencing project.
Is there a size limitation?
And should I save(keep) only the sequence I am interested in into
my_results instead of saving everything?
And is there a way of running some tests before doinr the blast_result.read()?
Now I try to use keep_hits=1 as a blast parameters in order to reduce
the size of my_result, will see.
Thanks for your time and help
Cheers,
yvan
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