Hi, I'm trying to install BLAST and use it on my local machine. I've installed BLAST, but I'm not quite sure why it isn't working - I've even tried throwing the blast executables (blastp, etc) and it doesn't seem to work. Here's and example output:
python myblastscript.py Running blastp, using min e-value, retrieving hits Extracted 1 features BLAST-ing gene_1 ID: gene_1 Name: <unknown name> Description: <unknown description> Number of features: 1 Seq('MDGRRSRHTDDTDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPAINAKRV...LEI', ExtendedIUPACProtein()) sh: blastp: command not found query cover: 0.151515151515 max_iden: 0.95 904667897 CSK81904.1 Uncharacterised protein [Shigella sonnei] 145 264 905276864 CSH89806.1 Uncharacterised protein [Shigella sonnei] >gi 145 264
Here's snips of what's not working, essentially the blast_cline works, but it's not recognizing blastp as a function.
def Blast_Features_Local(seqname): # open contents of seq file, add features from file of orfs # blast each file and return a single output table # loop through ORFs and print results in outFile blast_type="blastp" # set type of blast: n, p or x blast_db = "nr" # use nr for protein alignments blast_db_path = "/Users/username/Desktop/db/" min_evalue = 0.0001 max_hits = 5 #make a call to blast #create command line call to blast blast_cline = NcbiblastpCommandline(query='Temp.fasta', db=blast_db_path+blast_db, evalue=min_evalue, outfmt=5, out="temp_blast.xml", max_target_seqs = max_hits) os.system(str(blast_cline))
No idea why it's saying blastp command not found, I imported "from Bio.Blast.Applications import NcbiblastpCommandline" as well so I know that isn't the issue. Please help, thank you!!