ecodb_maker.py error

[foreignsand]

I use your ecodb_maker.py script regularly to create ecodb databases to test primers in silico. It's unbelievably helpful!

It still seems to be working perfectly well and is crating useable databases, but I get the following error when I run the script:

Reading taxonomy dump file...
List all taxonomy rank...
Sorting taxons...
Indexing taxonomy...
Indexing parent and rank...
Adding scientific name...
Adding taxid alias...
Adding deleted taxid...
Taxonomy compilation completed in: 0:04:18.990069
Writing database...
Skipped entry :
Traceback (most recent call last):
  File "/home/fw/dziedzie/local/bin/ecodb_maker.py", line 594, in <module>
    ecoDBWriter(args['output'], taxonomy, [args['input']])
  File "/home/fw/dziedzie/local/bin/ecodb_maker.py", line 574, in ecoDBWriter
    sys.stderr.write(sk + "\n")
TypeError: can only concatenate list (not "str") to list
        Full Command:                      /home/fw/dziedzie/local/bin/ecodb_maker.py -i vertebrate.refseq.fasta -t /nfs1/CGRB/BlastDB/NCBI/taxonomy/latest -o refseq_vertebrate_db 

I'm not sure what the complaint is about, I've tried replacing all newlines and I still get the same error. A subset of the file— appended with the .txt extension and edited to be small enough to upload—used for the command above is attached.

Any and all help would be much appreciated!

Cheers,
Emily
vertebrate.refseq.fasta.txt

[jimmyodonnell]

Holy moly, I had pretty much forgotten about this project, but I am very happy to hear you have found it useful!

It appears that sk is normally supposed to be a string, but for whatever reason here it's a list. You could explicitly convert it to a string by changing that line to read: sys.stderr.write(str(sk) + "\n"), and see if that at least lets you run the script without error? (In case you are not aware, that line is just printing output to screen when you run the script)