The bioBakery help forum

Appended headers in panphlan annotation files

Hi there! I’m using panphlan v3.1 and I’ve noticed that many of the annotation files I downloaded from Dropbox appear to have extra headers appended to the end of some lines. For example:

$ grep “NR90” panphlan_Escherichia_coli_annot.tsv | head -n 5
NR90 NR50 GO KO KEGG Pfam EC eggNOG
UniRef90_A0A0T5XRC3 UniRef50_A0A3A1V9Q0 PF06183 NR90 NR50 GO KO KEGG Pfam EC eggNOG
UniRef90_A0A0U4J0F4 UniRef50_A0A0U4J0F4 GO:0009401,GO:0016021 PF03613 NR90 NR50 GO KO KEGG Pfam EC eggNOG
UniRef90_A0A0U4J0F4 UniRef50_A0A0U4J0F4 GO:0009401,GO:0016021 K10986 cfar:CI104_03015 PF03613 NR90 NR50 GO KO KEGG Pfam EC eggNOG
UniRef90_A0A0U4J0F4 UniRef50_A0A0U4J0F4 GO:0009401,GO:0016021 K10986 eal:EAKF1_ch2793c PF03613 NR90 NR50 GO KO KEGG Pfam EC eggNOG

panphlan_download_pangenome.py wasn’t working for me (probably due to some aspect of how our cluster is configured) so I instead downloaded pangenomes from Dropbox here: Dropbox - panphlan_3_pangenomes_tar - Simplify your life
Is this the correct Dropbox link with the most recent versions of pangenomes and the corresponding annotation files?

I’m not sure if this causes panphlan to fail as I haven’t tried with the --func_annot option yet. I only noticed when trying to read the pangenome annotation files into R :slight_smile:

Many thanks,
Fiona

Hi,

indeed the duplication of header was an issue, I thought it had been corrected.
I’ll try to push a new version of the panphlan_clean_pangenome.py script in the coming days.
It is quicker than regenerating and re-uploading the full database

Sorry for the inconvenience, and thanks for reporting the issue

Léonard

A quick way to fix it though could be

sed -i 's/.NR90.*//' panphlan_Escherichia_coli_annot.tsv

That will replace all NR90 and the following character by empty text (so removing them) while preserving the first row

Thanks very much Leonard! I was indeed able to fix the annotation files as you suggested :slight_smile: Thank you for all you do to create and support these incredibly useful tools!

Fiona

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