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1 #!/bin/sh -e
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2
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3 SQLITE=$HOME/tools/sqlite3
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4 SQLITE=sqlite3
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5 OUT_FILE="sift.txt"
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6 OUT_SORT_FILE="sift.sort.txt"
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7 OUT_VCF="sift.vcf"
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8
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9 # Download files
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10 for f in Human_CHR1.sqlite.gz Human_CHR10.sqlite.gz Human_CHR11.sqlite.gz Human_CHR12.sqlite.gz Human_CHR13.sqlite.gz Human_CHR14.sqlite.gz Human_CHR15.sqlite.gz Human_CHR16.sqlite.gz Human_CHR17.sqlite.gz Human_CHR18.sqlite.gz Human_CHR19.sqlite.gz Human_CHR2.sqlite.gz Human_CHR20.sqlite.gz Human_CHR21.sqlite.gz Human_CHR22.sqlite.gz Human_CHR3.sqlite.gz Human_CHR4.sqlite.gz Human_CHR5.sqlite.gz Human_CHR6.sqlite.gz Human_CHR7.sqlite.gz Human_CHR8.sqlite.gz Human_CHR9.sqlite.gz Human_CHRX.sqlite.gz Human_CHRY.sqlite.gz Human_Supp.sqlite.gz Human_enst.sqlite.gz
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11 do
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12 url=ftp://ftp.jcvi.org/pub/data/sift/Human_db_37_ensembl_63/$f
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13 echo Getting file $url
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14 #wget $url
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15 done
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16
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17 # Unzip files
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18 for f in Human_CHR*.sqlite.gz
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19 do
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20 echo Decompressing file $f
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21 #gunzip $f
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22 done
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23
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24 # Dumping data
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25 rm -f $OUT_FILE
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26 for f in Human_CHR*.sqlite
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27 do
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28 echo Dumping Database $f to $OUT_FILE
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29
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30 TABLES=`$SQLITE $f ".tables" | tr "\n" "\t"`
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31 for t in $TABLES
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32 do
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33 echo " Dumping Table $t"
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34
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35 $SQLITE $f "select CHR, COORD1, NT1, NT2, SCORE, MEDIAN, SEQS_REP from $t where SCORE != '' AND NT1 != NT2;" \
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36 | tr "|" "\t" \
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37 | sed "s/^chr//" \
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38 >> $OUT_FILE
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39 done
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40 done
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41
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42 echo Sorting file
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43 sort -k 1 -n -k 2 -n -o $OUT_SORT_FILE $OUT_FILE
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44
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45 echo Creating VCF
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46 cat $OUT_SORT_FILE | sift2vcf.pl > $OUT_VCF
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47
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