Better README (#21)

* RFCT+DOC General_Scripts -> Resource_Generation

Also, improve the text of the README file

* DOC Add basic README in Manuscript_analysis

Author: luispedro

Manuscript_analysis/README.md

@@ -0,0 +1,24 @@
+# Manuscript analysis
+
+This directory contains the scripts to run the analysis and generate figures included in the GMSC manuscript. Each figure is associated with a Jupyter notebook
+
+## Installation
+
+The following command will create a conda environment with the necessary dependencies:
+
+
+```bash
+conda create \
+    -n gmsc_env \
+    python \
+    jupyter \
+    numpy \
+    pandas \
+    matplotlib \
+    geopandas \
+    scipy \
+    statsmodels \
+    biopython \
+    seaborn
+```
+

README.md

@@ -1,19 +1,21 @@
 # A catalogue of small proteins from the global microbiome
-This repository contains files and scripts to generate analysis and figures in the manuscript "A catalogue of small proteins from the global microbiome":
+
+This repository contains files and scripts to generate analysis and figures in the manuscript _A catalogue of small proteins from the global microbiome_:
+
 > Yiqian Duan, Celio Dias Santos-Junior, Thomas Sebastian Schmidt, Anthony Fullam, Breno L. S. de Almeida, Chengkai Zhu, Kuhn Michael, Xing-Ming Zhao, Peer Bork, Luis Pedro Coelho
-bioRxiv 2023.12.27.573469; doi: https://doi.org/10.1101/2023.12.27.573469
+> bioRxiv 2023.12.27.573469; doi: https://doi.org/10.1101/2023.12.27.573469
 
-The global microbial smORFs catalogue (GMSC) is available at https://gmsc.big-data-biology.org
+The results Global Microbial SMORFs Catalogue (GMSC) is available at https://gmsc.big-data-biology.org
 
-## Introduction
+## Structure
 
-The **General_Scripts** folder contains scripts to generate the GMSC resource.
+The folder `Resource_Generation` contains scripts to generate the GMSC resource from raw data. Note that this requires downloading all the contigs from [SPIRE](https://spire.embl.de) and [ProGenomes v2](https://progenomes2.embl.de/) as well as very large computational resources. The scripts are provided for transparency and reproducibility, but we recommend using the precomputed data (deposited at Zenodo or included here, see below) and the GMSC resource at https://gmsc.big-data-biology.org.
 
-The **Manuscript_Analysis** folder contains pre-computed files and scripts to run the analysis and generate figures included in the GMSC manuscript.
+The folder `Manuscript_Analysis` contains pre-computed files and scripts to run the analysis and generate figures included in the GMSC manuscript. The scripts are written in Python (depenencies listed below). Generally speaking, these do not require large computational resources and interested users can run them on their own machines and adapt them to perform follow-up analyses.
 
 ## Dependencies
 
-The softwares are required for the scripts.
+The following are required for the scripts (other versions may work, we list the ones that were used).
 
 | **Software** | **Availability** |
 | :---: | :---: |
@@ -24,7 +26,7 @@ The softwares are required for the scripts.
 | MMseqs2 | https://github.com/soedinglab/MMseqs2 |
 | Swipe (v.2.1.1) | https://github.com/torognes/swipe |
 | DIAMOND (v.2.0.4) | https://github.com/bbuchfink/diamond |
-| HMMer (v.3.3.2) | http://hmmer.org/ |
+| HMMer (v.3.3.2) | https://hmmer.org/ |
 | MAFFT (v.7.475) | https://mafft.cbrc.jp/alignment/software/ |
 | RNAcode (v.0.3) | https://github.com/ViennaRNA/RNAcode |
 | BWA (v.0.7.17) | https://github.com/lh3/bwa |
@@ -40,8 +42,8 @@ These databases are used in the construction and analysis of the catalogue.
 
 | **Database** | **Availability** |
 | :---: | :---: |
-| SPIRE | http://spire.embl.de |
-| ProGenomes v2 | http://progenomes2.embl.de/ |
+| SPIRE | https://spire.embl.de |
+| ProGenomes v2 | https://progenomes2.embl.de/ |
 | AntiFam (v.7.0) | ftp://ftp.ebi.ac.uk/pub/databases/Pfam/AntiFam/ |
 | PRIDE | https://www.ebi.ac.uk/pride/ |
 | RefSeq | https://ftp.ncbi.nlm.nih.gov/refseq/release/ |
@@ -50,6 +52,7 @@ These databases are used in the construction and analysis of the catalogue.
 
 ### Preprocessed data
 
-smORF catalogue & annotations: The smORF catalogue and its annotations are available at https://doi.org/10.5281/zenodo.7944370.
+smORF catalogue & annotations: The smORF catalogue and its annotations are available at https://doi.org/10.5281/zenodo.7944370
+
+Preprocessed data: For convenience, the preprocessed files are available under the `Manuscript_anlysis/data` folder.
 
-Preprocessed data: For convenience, the preprocessed files are available under the `Manuscript_anlysis/data` folder.