pygtftk

pygtftk copied to clipboard

AttributeError: 'Series' object has no attribute 'append'

1

Hi I am having the below mentioned issue while running gtftk ologram --more-bed option. ``` Traceback (most recent call last): File "/home2/s225347/.conda/envs/pygtftk/bin/gtftk", line 110, in args = main() File "/home2/s225347/.conda/envs/pygtftk/bin/gtftk",...

gyanmishra

Currently there is an issue with multithreading starting with 3.9. Need time to check...

dputhier

This PR was automatically created by Snyk using the credentials of a real user.Snyk has created this PR to fix one or more vulnerable packages in the `pip` dependencies of...

dputhier

ERROR-get_tx_seq : No genes were found on chromosomes defined in fasta file.

6

Hi, I'm using the get_tx_seq function from gtftk and I'm getting this error Here the header of my genome_fasta.fa file : >1 dna:chromosome chromosome:GRCm38:1:1:195471971:1 REF NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN...

yaskermezli

gtftk get_tx_seq: issue with chromosome names

1

The gtftk get_tx_seq command don't find chromosome when additional info is present in fasta file:

dputhier

At least for pandas and pybigwig.

dputhier

|-- 11:03-WARNING-profile : PlotnineError error, can not show group number: Aesthetics {'ha'} specified two times

2

In doc (section coverage): gtftk profile -D -i mini_real_tx.zip -g tx_classes -t tx_classes.txt -f bwig -o profile_tx -pf png -if example_07.png -w -nm ranging

dputhier

... and should be fixed.

dputhier

Just to improve robustness

dputhier

It would be interesting to create plugins to detect the various spicing events described in Hadas Keren, Galit Lev-Maor & Gil Ast (Alternative splicing and evolution: diversification, exon definition and...

dputhier