<<<>>> --> 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 <<<< PARA CONSEGUIR EL FRAGMENTO QUE QUEREMOS DE CADA PLASMIDO >>>> export SPC=''; #poner nombre de la especie export PLA=''; #poner nombre del plasmido while read gen ori end; do { echo "# Treballant amb $gen..."; o=`expr $ori - 1`; l=`expr $end - $ori + 1`; ( echo ">$gen $SPC"; /disc8/bin/fastachunk $PLA\_$SPC.fa $o $l ) > $gen.$PLA\_$SPC.fa; }; done <<'EOF' nombre coordenadasorigen coordenadasfinal # ejem. orf13 11478 12074 EOF <<<< OBTENCION DE DIFERENTES REGIONES DE CADA PLASMIDO >>>> --> pRi2659:.fa del gen, region intergenica, region singenica pRi2659_Arhizogenes.fa export SPC='Arhizogenes'; export PLA='pRi2659'; while read gen ori end; do { echo "# Treballant amb $gen..."; o=`expr $ori - 1`; l=`expr $end - $ori + 1`; ( echo ">$gen $SPC"; /disc8/bin/fastachunk $PLA\_$SPC.fa $o $l ) > $gen.$PLA\_$SPC.fa; }; done <<'EOF' ORF13 11478 12074 ORF13_syn 7826 13987 ORF13_in 10783 12538 ORF13_UPS 10977 11477 EOF --> pRi1724:.fa del gen, region intergenica, region singenica pRi1724_Arhizogenes.fa export SPC='Arhizogenes'; export PLA='pRi1724'; while read gen ori end; do { echo "# Treballant amb $gen..."; o=`expr $ori - 1`; l=`expr $end - $ori + 1`; ( echo ">$gen $SPC"; /disc8/bin/fastachunk $PLA\_$SPC.fa $o $l ) > $gen.$PLA\_$SPC.fa; }; done <<'EOF' ORF13 22254 22850 ORF13_syn 18621 24763 ORF13_in 21559 23315 ORF13_UPS 21753 22253 EOF --> pRi8195:.fa del gen, region intergenica, region singenica pRi8196_T-DNAorf10-14_Arhizogenes.fa export SPC='Arhizogenes'; export PLA='pRi8196'; export FRAG='T-DNAorf10-14'; while read gen ori end; do { echo "# Treballant amb $gen..."; o=`expr $ori - 1`; l=`expr $end - $ori + 1`; ( echo ">$gen $SPC"; /disc8/bin/fastachunk $PLA\_$FRAG\_$SPC.fa $o $l ) > $gen.$PLA\_$SPC.fa; }; done <<'EOF' ORF13 5940 6533 ORF13_syn 2406 8427 ORF13_in 5277 6963 ORF13_UPS 5439 5939 EOF