Blobtools goes straight to help

[bobbieshaban]

Hi,

I am trying to use blobtools and for the life of me I can't get it to get passed the help screen.

$ python create.py -i transcript-60_clean.fa -t blobplot.txt -x bestsum --nodes /Databases/Database/taxBlastdb/nodes.dmp --names /Databases/Database/taxBlastdb/names.dmp -b blobology.out.bam -y spades usage: blobtools create -i FASTA [-y FASTATYPE] [-o OUTFILE] [--title TITLE] [-b BAM...] [-s SAM...] [-a CAS...] [-c COV...] [--nodes ] [--names ] [--db ] [-t TAX...] [-x TAXRULE...] [-h|--help]

I've even put bestsum in quotes, can you please help me with what I am doing wrong? I'm sure I must have a typo somewhere.

If I try blobtools create I get the following python error.

./blobtools create -i transcript-60_clean.fa -t blobplot.txt -x "bestsum" --nodes /Databases/Database/taxBlastdb/nodes.dmp --names /Databases/Database/taxBlastdb/names.dmp -b blobology.out.bam -y spades Traceback (most recent call last): File "./create.py", line 36, in import lib.BtCore as bt File "~/lib/BtCore.py", line 97 'dict_of_blobs' : {name : blObj.dict for name, blObj in self.dict_of_blobs.items()}, ^ SyntaxError: invalid syntax

I am using python 2.7 $ python -V Python 2.7.8

[DRL]

Hi, are you running the latest version https://github.com/DRL/blobtools/releases/tag/v0.9.16 ?

create is executed by typing:

./blobtools create ...

the command below should work

./blobtools create \
-i transcript-60_clean.fa \
-t blobplot.txt \
-x bestsum \
--nodes /Databases/Database/taxBlastdb/nodes.dmp \
--names /Databases/Database/taxBlastdb/names.dmp \
-b blobology.out.bam \
-y spades

cheers,

dom

[bobbieshaban]

Hi,

Pretty sure I have the latest version, I git a syntax error after running that command.

[shabanb@melb-compute04 git]$ python27 ./blobtools create -i transcript-60_clean.fa -t blobplot.txt -x bestsum --nodes /Databases/Database/taxBlastdb/nodes.dmp --names /Databases/Database/taxBlastdb/names.dmp -b blobology.out.bam -y spades Traceback (most recent call last): File "./create.py", line 36, in import lib.BtCore as bt File "/data/Bioinfo/bioinfo-proj-bobbie/newProgs/blobTools/git/lib/BtCore.py", line 97 'dict_of_blobs' : {name : blObj.dict for name, blObj in self.dict_of_blobs.items()}, ^ SyntaxError: invalid syntax

[ksdiaz]

I just had this happen to me as well. I ran it earlier today and it worked fine, but on a second pipeline through, with the same BLAST taxfile, just filtered to remove low-confidence hits, blobtools is going straight to help on the blobtools view command. It executed blobtools create just fine. I have the latest version, but no errors occur at all, just straight to the help output. blobplot also executes just fine.

Edit to add: If I remove the usage section from view.py, I get the following python error: blobtools/view.py -i BlobDB.json -o NEM-A02_blobview.txt Traceback (most recent call last): File "/home/genome/kdiaz/programs/blobtools/view.py", line 16, in args = docopt(doc) File "/home/genome/kdiaz/programs/blobtools/docopt.py", line 555, in docopt usage_sections = parse_section('usage:', doc) File "/home/genome/kdiaz/programs/blobtools/docopt.py", line 467, in parse_section return [s.strip() for s in pattern.findall(source)] TypeError: expected string or buffer

I've tried looking up this problem but I'm not understanding how to fix it. It looks like it's only parsing usage, then exiting after printing usage to the screen before sending anything to process.

[DRL]

Hi, you are both not executing the programs as described in the manual. Please execute it as specified in the manual and let me know if the problem persists.

cheers,

dom

[ksdiaz]

As far as I can tell, I've been running it exactly as described in the manual. Is there an obvious error I made that I can't spot? I did get it running the first time, and when I repeated the command after that, I have been getting the straight-to-help "error" screen.

Thank you!

[DRL]

Hi ksfiaz,

execute "blobtools create" like this: `./blobtools create``

not like this: python create.py or python blobtools

cheers,

dom

[ksdiaz]

That was how I first encountered the error. I tried running it directly via the python script to see if I could debug it, but I couldn't figure out where the issue lay. When I run ./blobtools create I have no problem getting a BlobDB file, but when I run ./blobtools view I just get the help screen, even if I run all defaults and only input the BlobDB file.