notebook rename

README.md

@@ -3,14 +3,16 @@
 
 ## Initial Setup
 
-Clone this repository either via git CLI commands `git clone https://gitlab.tugraz.at/D5B8E35025578B91/ssn.git` or by manual download.
+Clone this repository either via git CLI `git clone https://gitlab.tugraz.at/D5B8E35025578B91/ssn.git` or by manual download.
 Check the input file format and then follow the instructions for the chosen analysis method.
 
+
 ## Input File
 
+
 ### Preliminary steps
 
-As described in the [chapter](https://www.youtube.com/watch?v=dQw4w9WgXcQ), the BLAST DB can be built with:
+As described in the [chapter](https://www.youtube.com/watch?v=dQw4w9WgXcQ), the BLAST database can be built with:
 ```bash
     makeblastdb -in FILE.fasta -dbtype prot -title TITLE -parse_seqids -out DATABASE
 ```
@@ -18,33 +20,32 @@ The all-vs-all BLAST is performed with:
 ```bash
     blastp -db DATABASE -query FILE.fasta -out FILE.tsv -outfmt "6 qseqid sseqid evalue bitscore"
 ```
-`FILE.tsv` is the output file used in the subsequent analysis to geenrate the SSN.
+FILE.tsv is the output file used in the subsequent analysis to geenrate the SSN.
+
 
 ## Analysis Scripts
 
+
 ### AWK
 
 The AWK script is meant to be operated from a GNU/Linux system shell.
 
 It must be run as:
-
 ```bash
     awk -f ssn.awk FILE.tsv 2> BITSCORES.csv > EVALUES.csv
 ```
-
-where the FILE.tsv is the input file, formatted as indicated in the **Input File** section, and the bitscores.csv and evalues.csv files containing the respective scores.
+where the FILE.tsv is the input file, formatted as indicated in the **Input File** section, and the BITSCORES.csv and EVALUES.csv files containing the respective scores.
 
 
 ### Python
 
-The python script requires a minimal python data analysis setup, with the pandas library to be installed via pip `pip install pandas -y` in your working environment.
+The python script requires a minimal python data analysis setup, with the pandas library to be installed via `pip install pandas -y` in your working environment.
 
 The analysis can then be launched from any shell as:
 ```bash
     python ssn.py --input FILE.tsv --bitscores BITSCORES.csv --evlaues EVALUES.csv
 ```
-
-where the FILE.tsv is the input file, formatted as indicated in the **Input File** section, and the bitscores.csv and evalues.csv files containing the respective scores.
+where the FILE.tsv is the input file, formatted as indicated in the **Input File** section, and the BITSCORES.csv and EVALUES.csv files containing the respective scores.
 
 
 ### Colab Notebook