https://github.com/sammyjava/pdcut

Routines for the PDcut project
https://github.com/sammyjava/pdcut

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Routines for the PDcut project

• Host: GitHub
• URL: https://github.com/sammyjava/pdcut
• Owner: sammyjava
• Created: 2022-02-01T17:23:47.000Z (almost 3 years ago)
• Default Branch: main
• Last Pushed: 2022-03-08T18:19:34.000Z (almost 3 years ago)
• Last Synced: 2024-11-11T09:50:13.531Z (2 months ago)
• Language: Shell
• Size: 13.6 MB
• Stars: 0
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# PDcut routines

## reformat-pho

This routine reformats the orthogroups in the `N0.tsv` file into a tab-delimited row format with only protein names.

For example, if you ran OrthoFinder in the At_Mus directory (containing the FASTAs), you'll get the following file:

```

At_Mus/OrthoFinder/Results_Feb01/Phylogenetic_Hierarchical_Orthogroups/N0.tsv

```

In this case, run reformat-pho as follows:

```

$ cd At_Mus/OrthoFinder/Results_Feb01/

$ ../../../reformat-pho > pho.tsv

```

This will create a file `pho.tsv` which contains the orthogroup identifiers, e.g.

```

HOG     OG      Gene Tree Parent Clade  Arabidopsis_thaliana.TAIR10.pep.all     Mus_musculus-Cilia_proteome

N0.HOG0000000   OG0000000       n0      AT5G09950.2     AT5G09950.3     AT5G09950.1     AT4G33170.1     AT1G16480.1 ...

```

Note that the top lines of this file are *very long* because they contain large At orthogroups. Groups that contain Mus genes are further down in the file.