Adds corrections to README.md

README.md

@@ -8,18 +8,20 @@ This repository contains code used in the Master's Thesis titled:
 
 - python3
 - biopython
+- numpy
+- R version 3+
 
 ## Usage
 
 ### analyse_gaf_genic.py
 
-Analyse the proportion of genic read bases aligned by GraphAligner.
+Analyse the proportion of genic read bases aligned by [Graphaligner](https://github.com/maickrau/GraphAligner).
 
 ```python analyse_gaf_genic.py gaffile blastfile reads.fa outfile.txt```
 
 Input/Output:
- - ```gaffile```: graphical alignment file produced by [Graphaligner](https://github.com/maickrau/GraphAligner)
- - ```blastfile```: [BLAST](https://www.sciencedirect.com/science/article/abs/pii/S0022283605803602?via%3Dihub) output file in tabular format generated from exact alignment of gene sequences from [Lees et al.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930550/) (aligned files are '*_dna.fa') to simulated genomes (```blastn -outfmt 6 -perc_identity 100 -qcov_hsp_perc 100```)
+ - ```gaffile```: graphical alignment file (GAF) produced by [Graphaligner](https://github.com/maickrau/GraphAligner)
+ - ```blastfile```: [BLAST](https://www.sciencedirect.com/science/article/abs/pii/S0022283605803602?via%3Dihub) output file in tabular format generated from exact alignment of gene sequences from [Lees et al.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5930550/) (aligned files are '*_dna.fa') to respective simulated genomes (```blastn -outfmt 6 -perc_identity 100 -qcov_hsp_perc 100```)
  - ```reads.fa```: read sequences used in alignment in FASTA format, generated by [Nanosim-H](https://github.com/karel-brinda/NanoSim-H)
  - ```outfile.txt```: output summary file
 
@@ -40,7 +42,7 @@ Analyse node length and degree from a GFA file.
 ```python analyse_nodes.py gfafile outpref```
 
 Input/Output
-- ```gfafile```: GFA file produced produced from graph construction
+- ```gfafile```: GFA file produced from graph construction
 - ```outpref```: output prefix for distribution and summary files
 
 ### analyse_unitig.py
@@ -58,10 +60,12 @@ Input/Output
 
 R script for analysis of output files from analyse_untig.py, generating unitig frequency plot.
 
-To use, specify input directory at ```#input directory```.
+To use, specify input directory at ```#input directory```, with files in .txt format.
 
 ### check_ORF.py
 
+This script contains two functions for analysing ORF calls made by a gene caller.
+
 #### check_ORF_in_ref()
 
 Checks presence of a called ORF in forward and reverse complements of a set of reference source sequences.
@@ -73,7 +77,7 @@ Input/Output
 - ```ref_fasta_for```: Multi-FASTA of reference source sequences (forward strand)
 - ```ref_fasta_rev```: Multi-FASTA of reference source sequences (reverse strand)
 - ```query_fasta```: ORF calls in FASTA format
-- ```outfasta```: output FASTA containing ORFs not present in forward or reverse sequences.
+- ```outfasta```: output FASTA containing ORFs not present in forward or reverse sequences
 
 #### check_ref_in_query()
 
@@ -89,14 +93,14 @@ Input/Output
 
 ### compare_gene_calls.py
 
-Compares known genes against called ORFs by Prodigal/ggCaller in S. pneumoniae capsular biosynthetic loci (CBL). Prints recall and precision, and returns list of unmatched sequences.
+Compares known genes against called ORFs by [Prodigal](https://github.com/hyattpd/Prodigal) or [ggCaller](https://github.com/samhorsfield96/ggCaller) in S. pneumoniae capsular biosynthetic loci (CBL). Prints recall and precision, and returns list of unmatched sequences.
 
 ```python compare_gene_calls.py reference_genes gene_calls caller_type group```
 
 Input/Output
 - ```reference_genes```: known genes in FASTA format
 - ```gene_calls```: ORF calls by [Prodigal](https://github.com/hyattpd/Prodigal) or [ggCaller](https://github.com/samhorsfield96/ggCaller) in FASTA format
-- ```caller_type```: specify which caller used (ggCaller = ggc, Prodigal = prod)
+- ```caller_type```: specify which gene caller used (ggCaller = ggc, Prodigal = prod)
 - ```group```: CBL group used in comparison.
 
 ### gfa_to_fasta.py
@@ -112,6 +116,6 @@ Input/Output
 
 ### panaroo_gene_freq.R
 
-R script for analysis of RTAB file generated by [Panaroo](https://github.com/gtonkinhill/panaroo)
+R script for analysis of RTAB file generated by [Panaroo](https://github.com/gtonkinhill/panaroo).
 
-For usage, specify input directory at ```#input directory```.
+For usage, specify input directory at ```#input directory```, with files in .RTAB format.