problems to makeblastdb, the fa file is not being recognised.

Question

[bio90029]

I have the above code to make a data base from different folder, and I am getting always the same error, 'contigs.fa' no recognized. I post my code, and hopefully someone can help me to find the error.

import glob, sys, os, subprocess
from Bio.Blast import NCBIXML
from Bio import SeqIO

def database_project():

    #folders where my data are store
    #looking for the files within the folder H*
    files = glob.glob('/home/my_name/velvet_results2/H*')
    for file in files:

        #looking for contigs.fa in each folder
        contigs=glob.glob(file + '/*.fa')
        print contigs


        #extract name of folder
        temporary_db = os.path.basename(file) 

        output= '/home/mu_name/velvet_results2/' + temporary_db +'_db'
        if os.path.exists(output):
            print 'This folder already exist'
        else:
            os.makedirs(output)


        cmd=['makeblastdb', '-in', 'contigs.fa', '-dbtype', 'nucl', '-out', 'temporary_db','-title', 'temporary_db']
        my_file=subprocess.Popen(cmd)
        my_file.wait()
        #return database_id
        print 'The database is done'
database_project()

Answer 1

[bio90029]

Thanks guys, I found the problem, glob.glob gives a list, in this case with one element. In the previous script, I was not telling which element to take. So I changed contgs.fa by contigs[0], and it worked perfectly.

cmd=['makeblastdb', '-in', contigs[0], '-dbtype', 'nucl', '-out', file + '/temporary_db','-title', 'temporary_db']

[st.ph.n]

Glad you figured it out, and learned something. I think your script can be condensed, and improved, but if it works, you're moving yourself forward with your skills.

Answer 2

[st.ph.n]

import glob, sys, os, subprocess
from Bio.Blast import NCBIXML
from Bio import SeqIO

def database_project():
    os.chdir('/home/my_name/velvet_results2')
    dirs = os.walk(os.getcwd())
    for d in dirs:
         os.chdir(d)
         for file in glob.glob('*.fa')
             temp_db = d.split('/')[-1] + '_db'

             try: 
                  os.mkdirs(temp_db)
             except OSError:
                  print 'The folder already exists.'

             os.chdir(temp_db)
             subprocess.call('makeblasdb -in contigs.fa -dbtype nucl', shell=True)

database_project()

[WouterDeCoster]

looks like you need a closing bracket in the line dirs = os.walk(os.getcwd()