Denis Puthier

icon indicating a website link https://tagc.univ-amu.fr/en/users/puthier-denis icon indicating an email [email protected]

icon company Aix Marseille Univ, INSERM, TAGC, UMR_S_1090, TGML, MarMaRa Institute icon location 13288 Marseille, France icon location Too short for a bio...

Results 13 comments of Denis Puthier

Problem with 'space' argument of facet_grid.

I had read the documentation and seen that this argument was not properly supported. But it was not clear to which extend it was... This is really problematic in the...

Problem with 'space' argument of facet_grid.

Hi, Do you plan to support this argument in the upcoming releases ?

divergent / convergent list of transcript

We should at least propose an argument to make it possible.

Blast output to GTF

This feature is now available in libgtftk. It will be integrated in future releases

gtftk get_tx_seq: issue with chromosome names

e.g. > 1 dna:tralalala...

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

Hi Yasmina, Yes. First, there is this issue related to " dna:chromosome chromosome:GRCm38:1:1:195471971:1 REF" which has not been fixed yet. This is a known issue (#171). But, yes, deleting every...

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

Also, you forgot to paste the error message. Denis

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

Ah yes, this error is handled. Maybe this is a story about a file having chr prefix not found in the other file ? Denis Le ven. 31 mars 2023...

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

I will reopen it as it should not complain for additional chromose in the fasta file (but for additional chromosome in the gtf file).

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

This could be related to pandas version. What is your current pandas version ? Could you try with 1.1.2 ? Best