Team 1 - Functional Annotation

List of scripts in our GitHub repo.

1. door2.pl -- script used to run door2
2. extractSequences.py -- a script which extracts sequences from a fasta file based on a headers given in second file
3. functionalAnnotationPipeline.sh -- the final pipeline
4. getFastaHeaders.sh -- script which extracts all headers from a fasta file and stores in a new file
5. outputParser.py -- script which parses the output of all tools, uClust and the original GFFs to create new GFFs with annotations
6. parseUclustOutput.py -- script which reads in the .uc file generated from uClust and creates an index file and a sizes file
7. pilerCr.sh -- script used to run pilerCR (not included in final pipeline)
8. reformatFasta.py -- script which changes the gene names in the fasta file, reformats the file so that all sequences are in 1 line and also appends the SRR ID in front of the gene name.
9. reformatGff.py -- script which changes column 1 of the GFF to the gene name and also appends the SRR ID in front of the gene name.

Other files in our GitHub repo are

1. kleb_all.opr
2. kleb_gid.txt
3. kop_final.table
4. protein_fasta_protein_homolog_model.fasta
5. VFDB_setB_nt.fas

These are the default databases used for door2, CARD and VFDB.