<<<<PARA CONSEGUIR LAS COORDENADAS DE LOS GENES EN CADA PLASMIDO>>>> 

# nos encontramos en: cd /home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO/GenBank 
export BIN=/home/u27910.est12.alu.upf/novell/home/Bioinformatica/TRABAJO/bin 

--> pRi2659 
perl $BIN/gb2gff.pl pRi2659_T-DNA_Arhizogenes.gb \ 
> ../Coordenadas/pRi2659_T-DNA_Arhizogenes.gene_coords_full 
correguido a mano 

--> pRi1724 
perl $BIN/gb2gff.pl pRi1724_Arhizogenes.gb \ 
> ../Coordenadas/pRi1724_Arhizogenes.gene_coords_full 

--> pRi8196 
perl $BIN/gb2gff.pl pRi8196_T-DNAorf10-14_Arhizogenes.gb \ 
> ../Coordenadas/pRi8196_T-DNAorf10-14_Arhizogenes.gene_coords_full 

--> pTiC58 
perl $BIN/gb2gff.pl pTiC58_Atumefaciens.gb \ 
> ../Coordenadas/pTiC58_Atumefaciens.gene_coords_full 

--> pRiA4 a mano 

--> pTi15955 
perl $BIN/gb2gff.pl pTi15955_T-DNA_Atumefaciens.gb \ 
> ../Coordenadas/pTi15955_T-DNA_Atumefaciens.gene_coords_full 

--> Streptomyces 
perl $BIN/gb2gff.pl Streptomyces.gb \ 
> ../Coordenadas/Streptomyces.gene_coords_full 

<<<< CREAMOS LOS FICHEROS gff DE CADA PLASMIDO >>>> 

--> pRi2659 
gawk '{ a="TDNA.pRi2659.Arhizo"; 
b="genbank_NCBI"; 
print a, b, "orf", $2, $3, ".", $4, "0", $1 } 
' ../Coordenadas/pRi2659_Arhizogenes.gene_coords_full \ 
> TDNA.pRi2659_Arhizogenes.genbank.gff 

--> pRi1724 
gawk '{ a="TDNA.pRi1724.Arhizo"; 
b="genbank_NCBI"; 
print a, b, "orf", $2, $3, ".", $4, "0", $1 } 
' ../Coordenadas/pRi1724_Arhizogenes.gene_coords_full \ 
> TDNA.pRi1724_Arhizogenes.genbank.gff 

--> pRi8196 
gawk '{ a="TDNA.pRi8196.Arhizo"; 
b="genbank_NCBI"; 
print a, b, "orf", $2, $3, ".", $4, "0", $1 } 
' ../Coordenadas/pRi8196_T-DNAorf10-14_Arhizogenes.gene_coords_full \ 
> TDNA.pRi8196_Arhizogenes.genbank.gff 

--> pTiC58 
gawk '{ a="TDNA.pTiC58.Atumefa"; 
b="genbank_NCBI"; 
print a, b, "orf", $2, $3, ".", $4, "0", $1 } 
' ../Coordenadas/pTiC58_Atumefaciens.gene_coords_full \ 
> TDNA.pTiC58_Atumefaciens.genbank.gff 

--> pRiA4 
gawk '{ a="TDNA.pRiA4.Arhizo"; 
b="genbank_NCBI"; 
print a, b, "orf", $2, $3, ".", $4, "0", $1 } 
' ../Coordenadas/pRiA4_Arhizogenes.gene_coords_full \ 
> TDNA.pRiA4_Atumefaciens.genbank.gff 

--> pTi15955 
gawk '{ a="TDNA.pTi15955.Atumef"; 
b="genbank_NCBI"; 
print a, b, "orf", $2, $3, ".", $4, "0", $1 } 
' ../Coordenadas/pTi15955_T-DNA_Atumefaciens.gene_coords_full \ 
> TDNA.pTi15955_Atumefaciens.genbank.gff 

--> Streptomyces 
gawk '{ a="Streptomyces"; 
b="genbank_NCBI"; 
print a, b, "orf", $2, $3, ".", $4, "0", $1 } 
' ../Coordenadas/Streptomyces.gene_coords_full \ 
> Streptomyces.genbank.gff