convertGenbank2table.py not running to completion with IMG-generated genbank files

[jcthrash]

Hello, I'm trying to convert my genbank files using convertGenbank2table.py. The genbank files were downloaded from IMG. The script does not finish, and never creates a genbank/ directory.

Command: $ ./convertGenbank2table.py -g SAR11_genbank/HTCC1062.gbk -v 2

Output/Error: /usr/local/packages/Python/2.7.3/gcc-4.4.6/lib/python2.7/site-packages/Bio/GenBank/Scanner.py:951: BiopythonParserWarning: Invalid indentation for sequence line warnings.warn("Invalid indentation for sequence line", BiopythonParserWarning) Text file saved as /project/jcthrash/tools/ITEP/raw/335992.2.txt Traceback (most recent call last): File "./convertGenbank2table.py", line 391, in fid = open(genbank_filename, "w") IOError: [Errno 2] No such file or directory: '/project/jcthrash/tools/ITEP/genbank/335992.2.gbk'

To try and comply with the input requirements, I've changed the titles to have 6 digit ids. However, this does not help:

$ ./convertGenbank2table.py -g SAR11_genbank/106234.gbk -v 2 -r

/usr/local/packages/Python/2.7.3/gcc-4.4.6/lib/python2.7/site-packages/Bio/GenBank/Scanner.py:951: BiopythonParserWarning: Invalid indentation for sequence line warnings.warn("Invalid indentation for sequence line", BiopythonParserWarning) WARNING: Backing up original gene output file /project/jcthrash/tools/ITEP/raw/335992.2.txt to location /project/jcthrash/tools/ITEP/335992.2.txt.bk in case something went wrong Text file saved as /project/jcthrash/tools/ITEP/raw/335992.2.txt Traceback (most recent call last): File "./convertGenbank2table.py", line 391, in fid = open(genbank_filename, "w") IOError: [Errno 2] No such file or directory: '/project/jcthrash/tools/ITEP/genbank/335992.2.gbk'

I will be happy to email the genbank file I'm using if you would like an example to work with.

Thanks in advance!

[mattb112885]

Greetings!

Sorry I think my previous response is irrelevant. This is happening because for some reason your genbank/ directory is missing (it should be part of the repository). If you create a genbank/ directory it should work. The idea is that you put your input in some other directory (aside from genbank/ ) and the script creates a copy of it in genbank/ with ITEP IDs added to it and with the expected nomenclature.

I added a check for the directory's existence to the script and create it if it is missing.

Matt

[jcthrash]

Hi Matt, Thanks for your prompt response. We downloaded the software on 3/20/14. Has it been updated since? I’ll make sure to try that again if so.

FYI, attached is one of the genbank files from IMG.

-jct

J. Cameron Thrash Assistant Professor Department of Biological Sciences Louisiana State University 225-578-8210 (office) http://thethrashlab.com Twitter: @DrJCThrash

On Apr 2, 2014, at 15:23, mattb112885 notifications@github.com wrote:

Actually also can you make sure you have the latest ITEP code? (CD do a 'git pull origin master'). I have fixed a couple of bugs in the convertGenbank2Table.py script since the initial release and this line

File "./convertGenbank2table.py", line 391, in fid = open(genbank_filename, "w")

is no longer line 391.

Best

Matt

— Reply to this email directly or view it on GitHub.

[mattb112885]

I edited my comment above because most likely old versions isn't the problem. Most likely the issue is that you need to have a genbank/ directory for one of the outputs to convertGenbankToTable.py (a modified Genbank file with ITEP IDs attached to each CDS), which for some reason was missing from your installation. I have edited the script to create it if it doesn't exist so if you update your ITEP it should hopefully work.

Best

Matt

[jcthrash]

Matt, That did solve almost everything, thank you!

Do I have any reason to worry about the following warning?

/usr/local/packages/Python/2.7.3/gcc-4.4.6/lib/python2.7/site-packages/Bio/GenBank/Scanner.py:951: BiopythonParserWarning: Invalid indentation for sequence line warnings.warn("Invalid indentation for sequence line", BiopythonParserWarning)

-jct

[mattb112885]

That just means the Genbank files from IMG don't conform to the genbank spec (which is a very common problem). You might want to make sure the sequences that get outputted to the file in raw/ are the same as the ones in the Genbank file, but if they are don't worry about it.

Glad it helped.

Matt

[mattb112885]

jct:

Did you get a lot of BAD messages when loading the genbank files? If you are using the contigs associated with genes you might want to make sure they're correct, I just fixed a bug on this. See issue #66 . Let me know if it runs into problems.

Matt