Gene Families and genetic maps Analyses Tools

• Author: Leiting Li
• Email: [email protected]
• Licence: BSD

This is a collection of tools for gene family, genetic maps and comparative genomics analyses.

Intallation

git clone https://github.com/lileiting/gfat.git

How to use

Shortcuts were supported for some of these scripts. For instance,

gfat.pl f f g

is equivalent to

gfat.pl formats fasta getseq

FASTA sequences

Print the ID for a FASTA sequence file in.fasta

gfat.pl formats fasta idlist in.fasta
cat in.fasta | gfat.pl formats fasta idlist
gfat.pl formats fasta idlist -i in.fasta
gfat.pl formats fasta idlist --input in.fasta

# With description
gfat.pl formats fasta idlist in.fasta -d
# Write results to a file
gfat.pl formats fasta idlist in.fasta -o idlist.txt

Print sequence length

gfat.pl formats fasta length in.fasta

Fetch sequences match a pattern

# Find WRKY genes
gfat.pl formats fasta motif in.fasta -p 'WRKYG[QK]K'
# Find sequences contain SSRs
gfat.pl formats fasta motif in.fasta -p '(([ATGC]{2,6}?)\2{3,})'

Get sequences based on sequence name

gfat.pl formats fasta getseq in.fasta -s gene1
gfat.pl formats fasta getseq in.fasta -s gene1 -s gene2
gfat.pl formats fasta getseq in.fasta -s gene1,gene2
gfat.pl formats fasta getseq in.fasta -p 'gene\d'
gfat.pl formats fasta getseq in.fasta -l list.txt
gfat.pl formats fasta getseq in.fasta -s gene1 -s gene2 -s gene3,gene4 -p 'name\d' -l list.txt

Acknowledgements

The scripts, functions and usage styles are largely inspired by Haibao Tang's JCVI utility libraries (Python based).

The scripts were also inspired by the p5-bpwrapper and other Perl based modules or scripts.