Bash_scripts

Overall Repository Decscription

Repository contains a slection of Bash shell scripts used during my MSc project for data management, merging and QC. Pertinent to AntiSMASH GenBank and Biosynthetic MetaSpades outputs.

Scripts useful in conjunction with

-AntiSMASH
https://antismash.secondarymetabolites.org/#!/start
https://doi.org/10.1093/nar/gkab335
-Biosynthetic MetaSpades
https://github.com/ablab/spades
https://dx.doi.org/10.1101%2Fgr.213959.116

Bash Script Descriptions

1. antismash_merger.sh

Merges GenBank files in respective AntiSMASH output folder into a single file.

2. antismash_multirun.sh

Runs AntiSMASH analysis tool on Biosynthetic MetaSpades processed fasta files; will run on each 'genecluster' fasta iteratively.

3. fasta_merge.sh

Merges Biosynthetic MetaSpades output fasta files to one file form their subdirectories and also pases out fasta read length data.

4. filesample_parse.sh

Compiles filename accessions together into one txt file from their base file name if in directory with several result folders and shows sample names used.

5. gbk_counter.sh

Useful during GenBank file management; counts number of GenBank files in curent directory.

6. gbk_read_counter.sh

Collects GenBank count data outputs from AntiSMASH into one file, breaks by common parsable marker and includes sample origin for use in analysis.

7. merge_scaffolds.sh

Merge scaffold fasta outputs from Biosynthetic MetaSpades into one unified file. Can be used further on fasta files with tweaking.

8. metaspades_fasta_merge.sh

Collects fastas together into one file, breaks by common parsable marker and includes fasta origin filename

9. remove_empty.sh

Removes empty files in all subdirectories; clears away and identifies failed ANtiSMASH/ Biosynthetic MetaSpades analyses