[Biopython] Bio.Blast.Applications issue with outfmt="quoted string"

[IRVIN, STEVEN (AG-Contractor/1000)]

Hello,

I am having an issue with the Biopython module making BLAST+ queries.

I am wondering if there is any support in Bio.Blast.Applications  for using the multiple arguments to -outfmt allowed by NCBI BLAST+ programs such as blastn.

I need to use this for example:

    blastn_cline = NcbiblastnCommandline(query='somefastafile.fas', db='tomato_cdna.db', evalue=1000, word_size=7, outfmt='10 qseqid sseqid length pident', out='outfile.txt')

The multiple arguments allowed to blastn -outfmt  allow the choice of specific columns output to the csv or tab separated file such subject_id, etc.

Biopython is returning non-zero exit status 1: USAGE when I run my program with above statement.


Here is a an example coomand line for BLAST+:

prompt_: blastn -query seq_fasta.fas -db local_db.db -out csv_out.csv -dust no -num_alignments 20 -num_descriptions 20 -evalue 1000 -word_size 7 -task blastn -outfmt "10 qseqid sseqid length pident"

I do not yet know if something in Bio.Blast.Applications needs to be modified to support this.

Steve

Steven D Irvin, MS
Bioinformatics Analyst
[cid:image003.png at 01CC1925.F25B8430] CC214-A
Monsanto Research Center
Chesterfield Village, MO
Steven.Irvin at monsanto.com<mailto:Steven.Irvin at monsanto.com>
(636) 737-1756


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