Closed tanghaibao closed 4 years ago
It seems that Phytozome has recently changed its FTP so the direct downloads may no longer work. I may have to work on a new downloader in the future.
Regarding your issues with running synteny analysis arabidopsis data, this is due to the gene names formatted in different fields in the downloaded gff file. This is a common issue.
$ python -m jcvi.formats.fasta format Athaliana_447_Araport11.cds.fa.gz -o athaliana.cds
$ python -m jcvi.formats.gff bed Athaliana_447_Araport11.gene.gff3.gz --key=Name -o athaliana.bed
$ python -m jcvi.compara.catalog ortholog athaliana athaliana
Please note that the additional flag --key=Name
when I formatted the gff to bed. The reason is that the gene names need to match between the formatted bed and cds file.
This is a sample line from the file Athaliana_447_Araport11.gene.gff3.gz
:
Chr1 phytozomev12 gene 3631 5899 . + . ID=AT1G01010.Araport11.447;Name=AT1G01010
The problem is that the ID=
gene name has some extra bits in it so the names no longer match, however luckily for us, the Name=
field contains the matching gene name. So we need to extract the properly field using --key=Name
when formatting gff => bed.
New Phytozome downloader enabled as of v0.9.13
.
Received from email on Nov-3-2019
Dear Dr. Tang,
Greetings!
I was trying to use jcvi to do synteny analysis, and encountered error reports as in attached files.
My system is centos 7, I used anaconda3 to create an environment for jcvi under python=2.7, and then installed jcvi with “conda install jcvi”.
After installation, I tried to download Phytozome datasets and failed [see Error report-1]. I thought it might be an internet problem, so I downloaded the genomes from Phytozome website (Phytozome 13) manually. Then, I used Athaliana to do the test. Processes in converting .cds.fas.gz and .gff3.gz files went well, but when performing syntenic analysis, there was an error report [Error report-2]. I also tried to perform the analysis under base environment (python 3.7, jcvi installed via pip), and similar error occurred [Error report-3].
Hope you can help me with some guides. The cds and gff files are also attached. Look forward to your reply and thank you very much!
Error report-1.docx Error report-2.docx Error report-3.docx