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Set up
$ . $TESTDIR/setup.sh
Set up the executable: samFilter.
$ EXEC=$TESTDIR/../samFilter
#Test samFilter with a *.sam file generated by blasr
$ OUTFILE=$OUTDIR/lambda_bax_filter_1.sam
$ STDFILE=$STDDIR/lambda_bax_filter_1.sam
$ TMP1=$OUTDIR/$$.tmp.out
$ TMP2=$OUTDIR/$$.tmp.stdout
$ rm -f $OUTFILE
$ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $OUTFILE --minAccuracy 70 --minPctSimilarity 30 --hitPolicy all
$ tail -n+7 $OUTFILE |sort > $TMP1
$ tail -n+7 $STDFILE |sort > $TMP2
$ diff $TMP1 $TMP2
$ rm $TMP1 $TMP2
#Test whether --minAccuracy and --minPctSimilarity can be float.
# $ rm -f $OUTFILE
# $ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $OUTFILE --minAccuracy 70.0 --minPctSimilarity 30.0 --hitPolicy all
# $ tail -n+7 $OUTFILE | sort > $TMP1
# $ tail -n+7 $STDFILE | sort > $TMP2
# $ diff $TMP1 $TMP2
# $ rm $TMP1 $TMP2
#Test samFilter with -hitPolicy allbest
$ OUTFILE=$OUTDIR/lambda_bax_filter_2.sam
$ STDFILE=$STDDIR/lambda_bax_filter_2.sam
$ rm -f $OUTFILE
$ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $OUTFILE --hitPolicy allbest
$ tail -n+7 $OUTFILE > $TMP1
$ tail -n+7 $STDFILE > $TMP2
$ diff $TMP1 $TMP2
$ rm $TMP1 $TMP2
#Test samFilter with --hitPolicy random
$ OUTFILE=$OUTDIR/lambda_bax_filter_3.sam
$ STDFILE=$STDDIR/lambda_bax_filter_3.sam
$ rm -f $OUTFILE
$ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $OUTFILE --hitPolicy random
$ tail -n+7 $OUTFILE > $TMP1
$ tail -n+7 $STDFILE > $TMP2
$ diff $TMP1 $TMP2
$ rm $TMP1 $TMP2
#Test samFilter with --hitPolicy randombest
$ OUTFILE=$OUTDIR/lambda_bax_filter_4.sam
$ STDFILE=$STDDIR/lambda_bax_filter_4.sam
$ rm -f $OUTFILE
$ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $OUTFILE --hitPolicy randombest
$ tail -n+7 $OUTFILE > $TMP1
$ tail -n+7 $STDFILE > $TMP2
$ diff $TMP1 $TMP2
$ rm $TMP1 $TMP2
# Test samFilter with --hitPolicy leftmost
$ OUTFILE=$OUTDIR/test_leftmost_out.sam
$ rm -f $OUTFILE
$ $EXEC $DATDIR/test_leftmost.sam $DATDIR/test_leftmost_target.fasta $OUTFILE --hitPolicy leftmost
$ tail -n+6 $OUTFILE |cut -f 4
1
$ OUTFILE=$OUTDIR/lambda_bax_filter_5.sam
$ STDFILE=$STDDIR/lambda_bax_filter_5.sam
$ rm -f $OUTFILE
$ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $OUTFILE
$ tail -n+7 $OUTFILE > $TMP1
$ tail -n+7 $STDFILE > $TMP2
$ diff $TMP1 $TMP2
$ rm $TMP1 $TMP2
#Test samFilter with --holeNumbers
$ OUTFILE=$OUTDIR/lambda_bax_filter_6.sam
$ STDFILE=$STDDIR/lambda_bax_filter_6.sam
$ rm -f $OUTFILE
$ $EXEC $DATDIR/lambda_bax.sam $DATDIR/lambda_ref.fasta $OUTFILE --holeNumbers 101350-105000,21494
$ tail -n+7 $OUTFILE > $TMP1
$ tail -n+7 $STDFILE > $TMP2
$ diff $TMP1 $TMP2
$ rm $TMP1 $TMP2
#Test samFilter with -filterAdapterOnly
$ $EXEC $DATDIR/filterAdapterOnly.sam $DATDIR/references/H1_6_Scal_6x/sequence/H1_6_Scal_6x.fasta $OUTDIR/filterAdapterOnly.sam -filterAdapterOnly $DATDIR/references/H1_6_Scal_6x/annotations/H1_6_Scal_6x_adapters.gff
$ tail -n+6 $OUTDIR/filterAdapterOnly.sam |cut -f 1,2,3,4
m130302_124313_42130_c100502672550000001523078308081365_s1_p0/10817\t16\t11k_plasmidbell_H1_6_Scal_6x\t29466 (esc)
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