Sequence table for Maize

[edeutsch]

Please independently create the same table for Maize

Plastid curl -O -R ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Proteomes/maize/plastid.2.fasta

Mitochondrion curl -O -R ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Proteomes/maize/mitochondrion.2.fasta

RefSeq curl -O -R ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Proteomes/maize/GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_protein.2.faa

B73_v5 curl -O -R ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Proteomes/maize/Zm-B73-REFERENCE-NAM-5.0_Zm00001eb.1.protein.2.fa

W22 curl -O -R ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Proteomes/maize/Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.protein.fa

UniProtKB curl -O -R ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Proteomes/maize/uniprot-proteome_UP000007305.2.fasta

ProFITS curl -O -R ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Proteomes/maize/ProFITS_TF_4a53_protein.2.remove.fasta

[edeutsch]

okay, I added 3 more files to the get_data.sh file for download, I think it is complete now. let's go with these titles and files in the order below:

B73_v5=Zm-B73-REFERENCE-NAM-5.0_Zm00001eb.1.protein.2.fa B73_v4=Zm-B73-REFERENCE-GRAMENE-4.0_Zm00001d.2.protein.2.fa UniProtKB=uniprot-proteome_UP000007305.2.fasta RefSeq=GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_protein.2.faa B73_v3=Zea_mays.AGPv3.22.pep.all.remove.2.fa W22_v2=Zm-W22-REFERENCE-NRGENE-2.0_Zm00004b.1.protein.fa ProFITS=ProFITS_TF_4a53_protein.2.remove.fasta AgriGO=agriGO_151.2.remove.fasta Mitochondrion=mitochondrion.2.fasta Plastid=plastid.2.fasta

Questions?

[MLi1104]

I checked the get_data.sh file from the maize folder, and I only see the original seven entries below:

I did a git pull to make sure and also checked in the repo. Maybe I am looking in the wrong file?

[edeutsch]

oops, you're right, I committed to the wrong branch!

Fixed now: https://github.com/PlantProteomes/SeqComparison/blob/main/proteomes/maize/original/get_data.sh

[MLi1104]

Cool, thanks!

[MLi1104]

Here is my table:

[KeshavGanapathyRaman]

Does anyone know why this bug keeps happening with my code? It's not recognizing my files locally at all even though they are there according to the directory. I'll also have a snippet of the table sent by tommorow

[edeutsch]

The error message shows that the open() statement is trying to open the whole parameter Title=Filename. You just want to open the Filename, not the Title=Filename

[KeshavGanapathyRaman]

https://docs.google.com/spreadsheets/d/1HzeNOGH4B9p0XA5qWoBNc5usgoZ-xQzG2H-xXKSJ1IA/edit?usp=sharing

Here is the attached spreadsheet, I believe the numbers are the same as Margaret's and I generally cross-referenced between both mine and her program.

As for the above message it was related to the arabidopsis matrix(whoops I didn't mean to post it here) and it did not recognize the location,but I think I got the solution.