---
# System prepended metadata

title: Combining UniProt counts
tags: [cov-irt]

---

---
tags: cov-irt
---

# Combining UniProt counts

[toc]

## Overview
This script takes tables that look like this:

```
1_SRR10903401  uniprot
11500          -
3403           P0C6V9
1244           P0C6W2
1191           E0XIZ2
...


1_SRR10903402  uniprot
22007          -
13805          P0C6V9
4961           E0XIZ2
4676           P0C6W2
...
```

And combines them into one like this:

```
uniprot        1_SRR10903401  1_SRR10903402
Not annotated  11500          22007
P0C6V9         3403           13805
P0C6W2         1244           4676
E0XIZ2         1191           4961
...
```

## Installing [covirt-micro](https://github.com/AstrobioMike/CoV-IRT-Micro) package in a conda environment

```bash
conda create -y -n covirt-micro -c conda-forge -c bioconda -c defaults -c astrobiomike covirt-micro

conda activate covirt-micro
```

## Getting example data

```
curl -L -o 01_SRR10903401_uniprot_id_counts.tsv https://osf.io/hmnyk/download

curl -L -o 01_SRR10903402_uniprot_id_counts.tsv https://osf.io/629fs/download
```

## Combining
It takes the multiple tables as a space delimited list, so can be called like so:

```bash
cov-combine-uniprot-ID-counts -i 01_SRR10903401_uniprot_id_counts.tsv 01_SRR10903402_uniprot_id_counts.tsv \
                              -o combined-UniProt-counts.tsv
```

Or with wildcards like so:

```bash
cov-combine-uniprot-ID-counts -i *.tsv -o combined-UniProt-counts.tsv
```

See `cov-combine-uniprot-ID-counts -h` or the top of the script file itself for more info.

<br>

> **NOTE**  
> As currently written, it will retain the sample identifier that is the first column header of the input file. If we want to be able to manipulate this, let me know 🙂

