segseq

A simple program that receives a GTF (Gene Transfer Format) file and a FASTA file and returns the sequences that matches with a specific annotated feature.

Software requirement

1. Haskell
2. Cabal
3. SQLite3: libsqlite3-dev

Installing SegSeq

1. Download segseq from GitHub

git clone https://github.com/myopdev/segseq.git

2. Execute cabal update

cabal update

3. Execute cabal install

cabal install ./segseq

4. Add the following line at the end of the .profile file

export PATH=$PATH:$HOME/.cabal/bin

Examples

Acceptor splice sites

segseq -r -x acceptor -f dataset/genes.fa -g dataset/genes.gtf -l 6 -o 3 > acceptor.fa

Donor splice sites

segseq -r -x donor -l 9 -o 3 -f dataset/genes.fa -g dataset/genes.gtf > donor.fa

CDS

segseq -r -x cds -f dataset/genes.fa -g dataset/genes.gtf

Intron

 segseq  -r -x intron -g dataset/genes.gtf -f dataset/genes.fa >

Initial Exons

segseq -r -x initial -g dataset/genes.gtf -f dataset/genes.fa

Internal Exons

segseq -r -x internal -g dataset/genes.gtf -f dataset/genes.fa

Final Exons

segseq -r -x final  -g dataset/genes.gtf -f dataset/genes.fa