I currently am able to generate a text file with the information but for some reason i can not send the data to go into a list. i have tried it 2 ways:
cnx = mysql.connector.connect(user='root', database='smor')
cursor = cnx.cursor()
sqlQuery = ("SELECT id,name,CAST(aa_seq as CHAR(65535)) aa_seq FROM smor.domain_tbl WHERE domain_type_id=5 AND domain_special IS NULL LIMIT 100000")
cursor.execute(sqlQuery)
print "Generating FASTA file: ", FASTA_File1
with open(FASTA_File1, "w") as FASTA1:
for (aa_id, name, aa_seq) in cursor:
FASTA1.write(">" + name + '\n' + aa_seq + '\n')
print ">" + name + '\n' + aa_seq
ListOfNames =[]
for (aa_id, name, aa_seq) in cursor:
ListOfNames.append(name)
cursor.close()
print "ListOfNames", ListOfNames
this successfully prints the name and amino acid sequence into the text file but the string is empty. here are the last lines of the output in the console:
>NC_018581.1_05_011_001_020 P
RVPGEMYERAEDGALIPTGVRARWVDAPGSRREIVGPIARHPRIDGRRVDLDVVEEALAAVTGVTAAAVVGLPTDDGVEVGACVVLDRDDLDVPGLRRELSQTLAAHCVPTMISIVESIPLGTDGRPDHGEV
ListOfNames []
As you can see the list remains empty. I thought that perhaps the cursor could not jump back up to the top so i closed the cursor and reopened it exactly as above but with the list generation in the second instance. this caused an error in the script and i do not know why.
Is it that the data can not be read directly into a list?
Theoretically i can split the names of the sequences back out of the text file but i am curious why this method is not working.
