Scripts used in "The genome of the yellow potato cyst nematode, Globoderia rostochiensis, reveals insights into the bases of parasitism and virulence"
- extractRegionFromCoordinates.py
Usage: ./extractRegionFromCoordinates.py [GFF] [FASTA] [US] [DS] [UE] [DE]
[GFF] : Intron features have to be present in GFF (use Genometools)
[US] : Positions upstream of start of intron feature in GFF
[DS] : Positions downstream of start of intron feature in GFF
[UE] : Positions upstream of end of intron feature in GFF
[DS] : Positions downstream of end of intron feature in GFF
- Extracting splice sites :
./extractRegionFromCoordinates.py nGr.v1.0.gff3 nGr.v1.0.fa 0 1 1 0
- rbbh.py
Usage: ./rbbh.py [BLAST1] [FASTA1] [BLAST2] [FASTA2] [EVAL] [COV]
[BLAST1] : BLAST result of G. pallida vs. G. rostochiensis
[FASTA1] : Protein sequences of G. pallida
[BLAST2] : BLAST result of G. rostochiensis vs. G. pallida
[FASTA2] : Protein sequences of G. rostochiensis
[EVAL] : Float of minimal evalue theshold of BLAST hit
[COV] : Float of minimal coverage threshold of BLAST hit
- parse_iadhore.py
Usage: ./parse_iadhore.py [GROS_BED] [GROS_LENGTH] [GPAL_BED] [GPAL_LENGTH] [ANCHORPOINTS] [BASECLUSTERS] [GROS_ASSEMBLY] [GPAL_ASSEMBLY]
[GROS_BED] : Bed file of G. rostochiensis
[GROS_LENGTH] : Length file of G. rostochiensis
[GPAL_BED] : Bed file of G. pallida
[GPAL_LENGTH] : Length file of G. pallida
[ANCHORPOINTS] : Anchorpoints file provided by i-ADHoRe
[BASECLUSTERS] : Baseclusters file provided by i-ADHoRe
[GROS_ASSEMBLY] : Assembly file of G. rostochiensis
[GPAL_ASSEMBLY] : Assembly file of G. pallida
- parse_snpeff.py
Usage : ./parse_snpeff.py [VCF.gz]
[VCF.gz] : Tabix indexed SNPeff VCF file