keep getting error with psiblast
hello
I am trying to calculate the PSSM but I keep getting error , where is the problem in this code ?
import os
import re
def command_pssm(content, output_file,pssm_file):
os.system('psiblast
-in_msa 1ak4.fasta
-db allseq.fasta
-num_threads 10
-num_iterations 3
-evalue 0.001
-out output_file
-out_ascii_pssm PSSM.txt' )
input_file = "1ak4.fasta"
output_file = "myoutput.txt"
out_ascii_pssm ="PSSM.txt"
command_pssm(input_file, output_file, out_ascii_pssm)
as an example I get the following error
BLAST query error: CAlnReader::GetSeqEntry(): Seq_entry is not available until after Read()
even when I run this command, I get the same error
psiblast -subject 1ak4.fasta -in_msa allseq.fasta -out_ascii_pssm pssm.txt
BLAST query error: CAlnReader::GetSeqEntry(): Seq_entry is not available until after Read()
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