/usr/share/bedtools/test/getfasta/test-getfasta.sh is in bedtools-test 2.25.0-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 | #!/bin/bash
# t.fa
# >chr1
# aggggggggg
# cggggggggg
# tggggggggg
# aggggggggg
# cggggggggg
BT=${BT-../../bin/bedtools}
check()
{
if diff $1 $2; then
echo ok
else
echo fail
fi
}
echo " getfasta.t01...\c"
LINES=$(echo $'chr1\t1\t10' | $BT getfasta -fi t.fa -bed stdin -fo - | awk 'END{ print NR }')
if [ "$LINES" != "2" ]; then
echo fail
else
echo ok
fi
echo " getfasta.t02...\c"
LEN=$($BT getfasta -split -fi t.fa -bed blocks.bed -fo stdout | awk '(NR == 2){ print length($0) }')
if [ "$LINES" != "2" ]; then
echo fail
else
echo ok
fi
echo " getfasta.t03...\c"
SEQ=$($BT getfasta -split -fi t.fa -bed blocks.bed -fo stdout | awk '(NR == 4){ print $0 }')
if [ "$SEQ" != "cta" ]; then
echo fail
else
echo ok
fi
# test -fo -
echo " getfasta.t04...\c"
SEQ=$($BT getfasta -split -fi t.fa -bed blocks.bed -fo - | awk '(NR == 4){ print $0 }')
if [ "$SEQ" != "cta" ]; then
echo fail
else
echo ok
fi
# test -split with -s -
echo " getfasta.t05...\c"
SEQ=$($BT getfasta -split -s -fi t.fa -bed blocks.bed -fo - | awk '(NR == 4){ print $0 }')
if [ "$SEQ" != "tag" ]; then
echo fail
else
echo ok
fi
# test -fullHeader
echo " getfasta.t06...\c"
LINES=$(echo $'chr1 assembled by consortium X\t1\t10' | $BT getfasta -fullHeader -fi t_fH.fa -bed stdin -fo - | awk 'END{ print NR }')
if [ "$LINES" != "2" ]; then
echo fail
else
echo ok
fi
# test without -fullHeader
echo " getfasta.t07...\c"
echo "WARNING. chromosome (chr1 assembled by consortium X) was not found in the FASTA file. Skipping." > exp
echo $'chr1 assembled by consortium X\t1\t10' | $BT getfasta -fi t_fH.fa -bed - -fo - 2> obs
check obs exp
rm obs exp
# test IUPAC
echo " getfasta.t08...\c"
echo \
">1:0-16
AGCTYRWSKMDVHBXN
>2:0-16
agctyrwskmdvhbxn" > exp
$BT getfasta -fi test.iupac.fa -bed test.iupac.bed -fo - > obs
check obs exp
rm obs exp test.iupac.fa.fai
# test IUPAC revcomp
echo " getfasta.t09...\c"
echo \
">1:0-16(-)
NXVDBHKMSWYRAGCT
>2:0-16(-)
nxvdbhkmswyragct" > exp
$BT getfasta -fi test.iupac.fa -bed test.iupac.bed -s -fo - > obs
check obs exp
rm obs exp test.iupac.fa.fai
# test the warning about an outdated FASTA index file
echo " getfasta.t10...\c"
echo \
">chr1
cggggggggg
>chr2
AAATTTTTTTTTT" > test.fa
# create an index file
echo -e "chr2\t2\t10" | $BT getfasta -fi test.fa -bed - -fo - > /dev/null
# modify the FASTA file in a second
sleep 1
touch test.fa
echo -e "chr2\t2\t10" | $BT getfasta -fi test.fa -bed - -fo - \
> /dev/null 2> obs
echo "Warning: the index file is older than the FASTA file." > exp
check obs exp
rm obs exp test.fa test.fa.fai
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