259 lines
6 KiB
Bash
Executable file
259 lines
6 KiB
Bash
Executable file
#!/bin/bash
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test_tmp=`tempfile`
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export test_tmp
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export LC_ALL=C
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opt_tester() {
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opt="$@"
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tmp=$(tempfile)
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test_2search() {
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xargs echo Search in < $tmp
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2search $opt $tmp 0 2 2.1 100000
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2search $opt -B $tmp 0 2 2.1 100000
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}
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(true) |
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sort $opt > $tmp
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echo Search in null file
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test_2search
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(echo) |
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sort $opt > $tmp
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echo Search in newline
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test_2search
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(echo 1.000000000) |
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sort $opt > $tmp
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test_2search
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(echo 1.000000000;
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echo 2) |
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sort $opt > $tmp
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test_2search
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(echo 1;
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echo 2.000000000) |
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sort $opt > $tmp
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test_2search
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(echo 1.000000000;
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echo 2;
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echo 3) |
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sort $opt > $tmp
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test_2search
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(echo 1;
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echo 2.000000000;
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echo 3) |
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sort $opt > $tmp
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test_2search
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(echo 1;
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echo 2;
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echo 3.000000000) |
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sort $opt > $tmp
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test_2search
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rm $tmp
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}
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export -f opt_tester
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test_n() {
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tmp=${test_tmp}_n
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true > $tmp
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echo Search in null file
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2search -n $tmp 0 2 2.1 100000
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2search -nB $tmp 0 2 2.1 100000
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echo > $tmp
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xargs echo Search in newline
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2search -n $tmp 0 2 2.1 100000
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2search -nB $tmp 0 2 2.1 100000
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echo 1.000000000 > $tmp
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xargs echo Search in < $tmp
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2search -n $tmp 0 2 2.1 100000
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2search -nB $tmp 0 2 2.1 100000
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echo 1.000000000 > $tmp
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echo 2 >> $tmp
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xargs echo Search in < $tmp
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2search -n $tmp 0 2 2.1 100000
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2search -nB $tmp 0 2 2.1 100000
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echo 1 > $tmp
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echo 2.000000000 >> $tmp
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xargs echo Search in < $tmp
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2search -n $tmp 0 2 2.1 100000
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2search -nB $tmp 0 2 2.1 100000
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echo 1.000000000 > $tmp
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echo 2 >> $tmp
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echo 3 >> $tmp
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xargs echo Search in < $tmp
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2search -n $tmp 0 2 2.1 100000
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2search -nB $tmp 0 2 2.1 100000
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echo 1 > $tmp
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echo 2.000000000 >> $tmp
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echo 3 >> $tmp
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xargs echo Search in < $tmp
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2search -n $tmp 0 2 2.1 100000
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2search -nB $tmp 0 2 2.1 100000
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echo 1 > $tmp
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echo 2 >> $tmp
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echo 3.000000000 >> $tmp
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xargs echo Search in < $tmp
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2search -n $tmp 0 2 2.1 100000
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2search -nB $tmp 0 2 2.1 100000
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rm $tmp
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}
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test_n_opt() {
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opt_tester -n
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}
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test_rn_opt() {
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opt_tester -rn
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}
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test_r_opt() {
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opt_tester -r
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}
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test_k3N_2N_1n() {
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tmp=$(tempfile)
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cat >$tmp <<EOF
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1 chr1 Sample 1
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11 chr1 Sample 1
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111 chr1 Sample 1
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1111 chr1 Sample 1
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11111 chr1 Sample 1
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111111 chr1 Sample 1
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1 chr2 Sample 1
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22 chr2 Sample 1
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111 chr2 Sample 1
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2222 chr2 Sample 1
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11111 chr2 Sample 1
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111111 chr2 Sample 1
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1 chr10 Sample 1
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11 chr10 Sample 1
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111 chr10 Sample 1
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1111 chr10 Sample 1
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11111 chr10 Sample 1
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111111 chr10 Sample 1
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1 chr1 Sample 2
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11 chr1 Sample 2
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111 chr1 Sample 2
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1111 chr1 Sample 2
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11111 chr1 Sample 2
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111111 chr1 Sample 2
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1 chr2 Sample 2
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22 chr2 Sample 2
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111 chr2 Sample 2
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2222 chr2 Sample 2
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11111 chr2 Sample 2
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111111 chr2 Sample 2
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1 chr10 Sample 2
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11 chr10 Sample 2
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111 chr10 Sample 2
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1111 chr10 Sample 2
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11111 chr10 Sample 2
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111111 chr10 Sample 2
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1 chr1 Sample 10
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11 chr1 Sample 10
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111 chr1 Sample 10
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1111 chr1 Sample 10
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11111 chr1 Sample 10
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111111 chr1 Sample 10
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1 chr2 Sample 10
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22 chr2 Sample 10
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111 chr2 Sample 10
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2222 chr2 Sample 10
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11111 chr2 Sample 10
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111111 chr2 Sample 10
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1 chr10 Sample 10
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11 chr10 Sample 10
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111 chr10 Sample 10
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1111 chr10 Sample 10
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11111 chr10 Sample 10
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111111 chr10 Sample 10
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EOF
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# Find the line with 111,chr2,Sample 10
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2grep -t '\t' -k3N,2N,1n $tmp 'Sample 10' chr2 111
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}
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test_partial_line() {
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tmp=$(tempfile)
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seq 100 | LC_ALL=C sort > $tmp
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echo '### 2search --grep'
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2search --grep $tmp 3
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echo '### 2grep'
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2grep $tmp 3
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echo '### ... | 2grep'
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echo 3 | 2grep $tmp
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rm $tmp
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}
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test_recstart() {
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tmp=$(tempfile)
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cat >$tmp <<EOF
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>sp|O14683|P5I11_HUMAN Tumor protein p53-inducible protein 11
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MIHNYMEHLERTKLHQLSGSDQLESTAHSRIRKERPISLGIFPLPAGDGLLTPDAQKGGET
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PGSEQWKFQELSQPRSHTSLKVSNSPEPQKAVEQEDELSDVSQGGSKATTPASTANSDVAT
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IPTDTPLKEENEGFVKVTDAPNKSEISKHIEVQVAQETRNVSTGSAENEEKSEVQAIIEST
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PELDMDKDLSGYKGSSTPTKGIENKAFDRNTESLFEELSSAGSGLIGDVDEGADLLGMGRE
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VENLILENTQLLETKNALNIVKNDLIAKVDELTCEKDVLQGELEAVKQAKLKLEEKNRELE
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EELRKARAEAEDARQKAKDDDDSDIPTAQRKRFTRVEMARVLMERNQYKERLMELQEAVRW
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TEMIRASRENPAMQEKKRSSIWQFFSRLFSSSSNTTKKPEPPVNLKYNAPTSHVTPSVX
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>sp|P04637|P53_HUMAN Cellular
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IQVVSRCRLRHTEVLPAEEENDSLGADGT
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PQLX
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>sp|P10144|GRAB_HUMAN Granzyme B OS=Homo sapiens OX=9606
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MQPILLLLAFLLLPRADAGEIIGGHEAKPHSRPYMAYLMIWDQKSLKRCGGFLIRD
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WGSSINVTLGAHNIKEQEPTQQFIPVKRPIPHPAYNPKNFSNDIMLLQLERKAKRT
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SNKAQVKPGQTCSVAGWGQTAPLGKHSHTLQEVKMTVQEDRKCEX
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>sp|P13674|P4HA1_HUMAN Prolyl
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VECCPNCRGTGMQIRIHQIGPGMVQQIQS
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DGQKITFHGEGDQEPGLEPGDIIIVLDQK
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SHPGQIVKHGDIKCVLNEGMX
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>sp|Q06416|P5F1B_HUMAN Putative POU domain, class 5, transc
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IVVKGHSTCLSEGALSPDGTVLATASHDGYVKFWQIYIEGQDEPRCLHEWKP
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HDGRPLSCLLFCDNHKKQDPDVPFWRFLITGADQNRELKMWCTVSWTCLQTI
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RFSPDIFSSVSVPPSLKVCLDLSAEYLILSDVQRKVLYVMELLQNQEEGHAC
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FSSISEFLLTHPVLSFGIQVVSRCRLRHTEVLPAEEENDSLGADGTHGAGAX
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>sp|Q7Z4N8|P4HA3_HUMAN
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MTEQMTLRGTLKGHNGWVTQIA
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YGIPQRALRGHSHFVSDVVISS
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GHTKDVLSVAFSSDNRQIVSGS
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VRFSPNSSNPIIVSX
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>sp|Q96A73|P33MX_HUMAN Putative
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RNDDDDTSVCLGTRQCSWFAGCTNRTWNSSA
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VPLIGLPNTQDYKWVDRNSGLTWSGNDTCLY
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SCQNQTKGLLYQLFRNLFCSYGLTEAHGKWR
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CADASITNDKGHDGHRTPTWWLTGSNLTLSV
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NNSGLFFLCGNGVYKGFPPKWSGRCGLGYLV
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PSLTRYLTLNASQITNLRSFIHKVTPHRX
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>sp|Q9UHX1|PUF60_HUMAN Poly(U)-binding-splicing
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MGKDYYQTLGLARGASDEEIKRAYRRQALRYHPDKNKEPGAEEKFKE
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IAEAYDVLSDPRKREIFDRYGEEGLKGSGPSGGSGGGANGTSFSYTF
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HGDPHAMFAEFFGGRNPFDTFFGQRNGEEGMDIDDPFSGFPMGMGGF
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TNVNFGRSRSAQEPARKKQDPPVTHDLX
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EOF
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echo "--regstart"
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echo start
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2search -t '\|' -k2 --recstart '>' $tmp O14683
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echo middle
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2search -t '\|' -k2 --recstart '>' --recend '' $tmp Q96A73
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echo end
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2search -t '\|' -k2 --recstart '>' $tmp Q9UHX1
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echo "--regstart + --regend"
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echo start
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2search -t '\|' -k2 --recstart '>' --recend '\n' $tmp O14683
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echo middle
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2search -t '\|' -k2 --recstart '>' --recend '\n' $tmp Q96A73
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echo end
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2search -t '\|' -k2 --recstart '>' --recend '\n' $tmp Q9UHX1
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rm $tmp
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}
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export -f $(compgen -A function | grep test_)
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compgen -A function | grep test_ | sort | parallel -j6 --tag -k '{} 2>&1' > regressiontest.new
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diff -Naur regressiontest.new regressiontest.out
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