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3
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1 #!/bin/sh
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2
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3 # wget ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/wgs/assembly/build_2.40/S_lycopersicum_chromosomes.2.40.fa.gz
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4
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5 # GFF has to be downloaded manually from
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6 #
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7 # http://solgenomics.net/itag/release/2.3/list_files#
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8 # File ITAG2.3_gene_models.gff3
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9 #
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10 #
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11
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12 # Create genes.gff
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13 echo Decompressing the file
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14 cp ITAG2.3_gene_models.gff3.gz genes.gff.gz
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15 rm -f genes.gff
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16 gunzip genes.gff.gz
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17
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18 echo Fixing start-end problem
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19 cat genes.gff | ./fixStartEnd.pl > g
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20 mv g genes.gff
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21
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22 # Append FASTA Sequences
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23 echo "###" >> genes.gff
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24 echo "##FASTA" >> genes.gff
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25 zcat S_lycopersicum_chromosomes.2.40.fa.gz >> genes.gff
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26
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