Lisa K. Johnson
Lisa K. Johnson
Working on https://github.com/dib-lab/khmer/issues/998, using this command: > ./setup.py nosetests --tests tests/test_scripts.py:test_load_graph_multithread default args: > args = ['-N', '4', '-x', '1e7', '-T', '8', outfile, infile] (ran ~ 20 x) displayed 4...
Hello, thank you for this useful package! I like the ability to condense many venn diagrams down into one visualization. I'm having a problem displaying all intersections between 17 sets....
trying to clone a repository, error: ``` (ONT) johnsolk@barbera:~$ osf -p zjv86 clone 59files [11:54, 2.21s/files] Traceback (most recent call last):####################################################################################################################################| 543/543 [00:00
It seems that after uploading a set of directories within directories to an osf project, the beginning part of the directory name,`A_xenica` is being truncated from each. Presumably because the...
Something weird is going on with the `GFF3Parser`. I think something is happening on df concatenation step? These are gff3 generated with master version of dammit, new shmlast=1.4 and 3...
Not sure if this is a dammit problem, seems like a disk space issue. parallel during lastall seemed unhappy with long records: ``` # dammit ## a tool for easy...
With `conda install dammit` version on hpc bridges, only 1 custom aa database: ``` [ljcohen@br018 sbatch_files]$ cat dammit_L_parva-4642625.o # dammit ## a tool for easy de novo transcriptome annotation by...
``` # dammit ## a tool for easy de novo transcriptome annotation by Camille Scott **v1.0rc2**, 2018 ## submodule: annotate ### Database Check #### Info * Database Directory: /pylon5/bi5fpmp/ljcohen/dammit *...
Can dammit output this table? A table is required by [tximport](https://www.bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html) to [convert between transcript ID and gene](https://f1000research.com/articles/4-1521/) [Example table file](https://github.com/ngs-docs/2017-dibsi-rnaseq/blob/master/nema_gene_name_id.csv) Made by [tutorial](https://dibsi-rnaseq.readthedocs.io/en/latest/dammit_annotation.html): ``` import pandas as pd from...
``` >>> import pandas as pd >>> from dammit.fileio.gff3 import GFF3Parser >>> gff_file = "trinity.nema.fasta.dammit.gff3" >>> annotations = GFF3Parser(filename=gff_file).read() /home/ljcohen/py3/lib/python3.5/site-packages/dammit/fileio/gff3.py:68: ParserWarning: Both a converter and dtype were specified for column...