Hi All!

I am trying to build a blast database using an input fasta file. I am doing this with subprocess, rather than from the command line, as I'm making a reciprocal best hit pipeline. I have a pre-computed BLAST+ makeblastdb database against which the user's input sequences are blasted, and then I need all of the input sequences to be turned into a database in turn, against which the best hits of the previous BLAST run can be BLASTed (i.e. it needs to take whatever the user inputs, on a case by case basis, programatically). Sequences that 'hit' and/or don't 'hit' each other are then labelled appropriately.

Subprocess code:

import subprocess

def run_process(cmd):
    if type(cmd)==list:
        shell_bool=False
    elif type(cmd)==str:
        shell_bool=True
    else:
        return 'Bad input cmd'
    try:
        cmd = subprocess.run(cmd, check=True, capture_output=True, shell=shell_bool)
        return cmd
    except FileNotFoundError as e1:
        print ('FileNotFoundError:')
        print ('\n', e1)
        return e1
    except subprocess.CalledProcessError as e2:
        print ('CalledProcessError:')
        print ('\n',e2)
        print ('\n',e2.stderr)
        print ('\n',e2.stdout)
        return e2

db_type_str=' -dbtype prot'
makeblastdb_path= r'"C:\Users\u03132tk\.spyder-py3\modulesData\NCBI\blast-2.10.1+\bin\makeblastdb.exe"'
fasta_db_path= r' -in "C:\Users\u03132tk\.spyder-py3\modulesData\fasta_sequences_SMCOG_efetch_only.txt"'

cmd_str=makeblastdb_path + fasta_db_path + db_type_str
#std_err = Error: mdb_env_open: There is not enough space on the disk.

cmd1=[makeblastdb_path, fasta_db_path, db_type_str] 
#-->[WinError 2] The system cannot find the file specified

cmd2=[makeblastdb_path + fasta_db_path + db_type_str]
#-->PermissionError: [WinError 5] Access is denied

test=run_process(cmd_str) 
#or cmd1 or cmd2

I've been looking into subprocess and think my code should work, but whilst I've tried inputting the command as a string (cmd_str) and as a list (cmd), and for cmd values either as one big string ([makeblastdb_path + fasta_db_path + db_type_str]) or as separate arguments ([makeblastdb_path, fasta_db_path, db_type_str]), neither work.

I've most progress using cmd_str - it does seem to start running makeblastdb. However, I get CalledProcessError with return code 255, and stderr is Error: mdb_env_open: There is not enough space on the disk. Whilst this seems like a clear cut issue, when I copy cmd_str into command line it works fine, suggesting disk space isnt the problem. Any ideas why this is?

I have already made the BLASTDB_LMDB_MAP_SIZE=1000000 environment variable as discussed here makeblastdb Fasta file with 25 sequences gives Error: mdb_env_open: There is not enough space on the disk, but I don't think this is the issue, due to my successful command line runs and the different environment variables (mdb_env_open vs BLASTDB_LMDB_MAP_SIZE).

Cheers for reading!

Tim

EDIT 1 - Working code:

import subprocess
import os 

def run_process(cmd):
    if type(cmd)==list:
        shell_bool=False
    elif type(cmd)==str:
        shell_bool=True
    else:
        return 'Bad input cmd'
    envp = {
        **os.environ,
        'BLASTDB_LMDB_MAP_SIZE':'1000000',
    }
    print (envp)
    try:
        cmd = subprocess.run(cmd, check=True, capture_output=True, shell=shell_bool, env=envp)
        return cmd
    except FileNotFoundError as e1:
        print ('FileNotFoundError:')
        print ('\n', e1)
        return e1
    except subprocess.CalledProcessError as e2:
        print ('CalledProcessError:')
        print ('\n',e2)
        print ('\n',e2.stderr)
        print ('\n',e2.stdout)
        return e2

db_type_str='prot'
makeblastdb_path= r'C:\Users\u03132tk\.spyder-py3\modulesData\NCBI\blast-2.10.1+\bin\makeblastdb.exe'
fasta_db_path= r'C:\Users\u03132tk\.spyder-py3\modulesData\fasta_sequences_SMCOG_efetch_only.txt'

cmd1=[makeblastdb_path, '-in', fasta_db_path, '-dbtype', db_type_str]
test=run_process(cmd1)