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2: We need three extra steps for the database parsing scripts to work.
i) gunzip VFDB_setB_nt.fas.gz
ii) mv VFDB_setB_nt.fas VFDB_setB_nt.fas.ffn
iii) save the following code as convert.py and execute as python convert.py, which gets rid of the "(gi:xxxxx)" bit in the sequence headers and the commas (replacing with '_') because downstream processing splits on the commas:
with open("VFDB_setB_nt.fas.ffn", "r") as input_handle:
with open("VFDB_setB_nt.fas_corrected.ffn", "w") as output_handle:
for line in input_handle:
if '(gi:' in line:
line=line.replace('(gi:', ' (gi:').replace(',','_')
line = line.split()
output_handle.write(line[0]+' '+' '.join(line[2:])+'\n')
else:
output_handle.write(line)
Without removing the text "(gi:xxxxx)" from the header, this next step will not work:
Also, there is a redundant comment on line 46 in the script VFDB_cdhit_to_csv.py (should read "VFGxxxxxx"):
schultzm@x:gene_dbs $ grep 'the unique ID R0xxx' ~/VFDB_cdhit_to_csv.py -n
46: database[ClusterNr].append(seqID) # for virulence gene DB, this is the unique ID R0xxx
The text was updated successfully, but these errors were encountered:
Actually, it's a bit more than the above. Need to remove the whole "(gi:xxxxxxxx)" bit. Here's how I did it using python:
with open("VFDB_setB_nt.fas.ffn", "r") as input_handle:
with open("VFDB_setB_nt.fas.ffn_edit", "w") as output_handle:
for line in input_handle:
if ' (gi:' in line:
line = line.split()
output_handle.write(line[0]+' '+' '.join(line[2:])+'\n')
else:
output_handle.write(line)
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Error in step: Using the VFDB Virulence Factor Database with SRST2
1: The URL to the VFDB has changed and, using wget, should now be:
wget http://www.mgc.ac.cn/VFs/Down/VFDB_setB_nt.fas.gz
2: We need three extra steps for the database parsing scripts to work.
i)
gunzip VFDB_setB_nt.fas.gz
ii)
mv VFDB_setB_nt.fas VFDB_setB_nt.fas.ffn
iii) save the following code as convert.py and execute as
python convert.py
, which gets rid of the "(gi:xxxxx)" bit in the sequence headers and the commas (replacing with '_') because downstream processing splits on the commas:Without removing the text "(gi:xxxxx)" from the header, this next step will not work:
Also, there is a redundant comment on line 46 in the script VFDB_cdhit_to_csv.py (should read "VFGxxxxxx"):
The text was updated successfully, but these errors were encountered: