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3
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1 #!/bin/sh -e
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2
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3 echo "Processing GFF file"
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4 gunzip -c Gmax_109_gene.gff3.gz > genes.gff
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5 # | sed "s/.five_prime_UTR.1//" \
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6 # | sed "s/.three_prime_UTR.1//" \
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7 # > genes.gff
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8
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9 echo "Adding FASTA sequence"
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10 ( echo "###" ; echo "##FASTA" ; gunzip -c Gmax_109.fa.gz ) >> genes.gff
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11
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12 ehco "Create CDS file"
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13 gunzip -c Gmax_109_cds.fa.gz \
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14 | sed "s/|PACid:/|PAC:/" \
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15 | sed "s/Glyma.*|//" \
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16 > cds.fa
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17
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18 echo "Create protein file"
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19 gunzip -c Gmax_109_peptide.fa.gz \
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20 | sed "s/|PACid:/|PAC:/" \
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21 | sed "s/Glyma.*|//" \
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22 > protein.fa
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23
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24 # Build databse
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25 cd $HOME/snpEff
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26
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27 ./scripts/snpEffM.sh build -v -gff3 gmax1.09v8 2>&1 | tee gmax1.09v8.build
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28
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29 # CDS test
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30 ./scripts/snpEffM.sh cds -v gmax1.09v8 data/gmax1.09v8/cds.fa 2>&1 | tee gmax1.09v8.cds
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31
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32 cd -
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33
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34 echo Done!
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35
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