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|
Set up directories
$ . $TESTDIR/setup.sh
Set up the executable: loadPulses.
$ EXEC=$TESTDIR/../loadPulses
#Test loadPulses: input is a pls.h5 file
#Test -byread and -bymetric
$ PLS_IN=$DATDIR/ecoli_lp.fofn
$ CMP_IN_2=$DATDIR/ecoli_lp_tiny.cmp.h5
$ CMP_STDOUT_2=$STDDIR/ecoli_lp_tiny.cmp.h5
$ CMP_OUT_byread_2=$OUTDIR/ecoli_lp_tiny.byread.cmp.h5
$ CMP_OUT_bymetric_2=$OUTDIR/ecoli_lp_tiny.bymetric.cmp.h5
$ METRICS=StartFrame,PulseWidth,WidthInFrames,pkmid,IPD,Light
$ rm -f $CMP_OUT_byread_2
$ cp $CMP_IN_2 $CMP_OUT_byread_2
$ $EXEC $PLS_IN $CMP_OUT_byread_2 -metrics $METRICS -byread
[INFO] * [loadPulses] started. (glob)
loading 2 alignments for movie 1
loading 2 alignments for movie 2
[INFO] * [loadPulses] ended. (glob)
$ h5diff -c $CMP_OUT_byread_2 $CMP_STDOUT_2
dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
\d+ differences found (re)
dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
\d+ differences found (re)
[1]
$ rm -f $CMP_OUT_bymetric_2
$ cp $CMP_IN_2 $CMP_OUT_bymetric_2
$ $EXEC $PLS_IN $CMP_OUT_bymetric_2 -metrics $METRICS -bymetric
[INFO] * [loadPulses] started. (glob)
loading 2 alignments for movie 1
loading 2 alignments for movie 2
[INFO] * [loadPulses] ended. (glob)
$ h5diff -c $CMP_OUT_bymetric_2 $CMP_STDOUT_2
dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
\d+ differences found (re)
dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
\d+ differences found (re)
[1]
#Test loadPulses for deep sorted cmp.h5
$ FOFN_IN=$DATDIR/ecoli_lp.fofn
$ CMP_IN_SORTED=$DATDIR/ecoli_lp_tiny_sorted.cmp.h5
$ CMP_STDOUT_SORTED=$STDDIR/ecoli_lp_tiny_sorted.cmp.h5
$ CMP_OUT_SORTED_bymetric=$OUTDIR/ecoli_lp_tiny_sorted_bymetric.cmp.h5
$ CMP_OUT_SORTED_byread=$OUTDIR/ecoli_lp_tiny_sorted_byread.cmp.h5
$ METRICS=StartFrame,PulseWidth,WidthInFrames,pkmid,IPD,Light,DeletionQV,InsertionQV,SubstitutionQV,MergeQV,QualityValue,DeletionTag,SubstitutionTag,ClassifierQV,PreBaseFrames,PulseIndex
$ rm -f $CMP_OUT_SORTED_bymetric
$ cp $CMP_IN_SORTED $CMP_OUT_SORTED_bymetric
$ $EXEC $FOFN_IN $CMP_OUT_SORTED_bymetric -bymetric -metrics $METRICS > $OUTDIR/tmp.log
[INFO] * [loadPulses] started. (glob)
[INFO] * [loadPulses] ended. (glob)
$ h5diff -c $CMP_OUT_SORTED_bymetric $CMP_STDOUT_SORTED
dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
\d+ differences found (re)
dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
\d+ differences found (re)
[1]
$ rm -f $CMP_OUT_SORTED_byread
$ cp $CMP_IN_SORTED $CMP_OUT_SORTED_byread
$ $EXEC $FOFN_IN $CMP_OUT_SORTED_byread -byread -metrics $METRICS > $OUTDIR/tmp.log
[INFO] * [loadPulses] started. (glob)
[INFO] * [loadPulses] ended. (glob)
$ h5diff -c $CMP_OUT_SORTED_bymetric $CMP_STDOUT_SORTED
dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
\d+ differences found (re)
dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
\d+ differences found (re)
[1]
#Test loadPulses for a zero-alignment cmp.h5 file.
$ FOFN_IN=$DATDIR/ecoli_lp.fofn
$ CMP_IN_NOALN=$DATDIR/noaln_lp.cmp.h5
$ $EXEC $FOFN_IN $CMP_IN_NOALN -byread -metrics $METRICS
[INFO] * [loadPulses] started. (glob)
WARNING, there is no alignment in the cmp file.
[INFO] * [loadPulses] ended. (glob)
#Test loadPulses -byMetric with a 'large' bas.h5 file of which the dataset size is greater than maxElements.
$ FOFN_IN=$DATDIR/ecoli_lp.fofn
$ CMP_IN=$DATDIR/ecoli_lp_tiny_sorted.cmp.h5
$ CMP_OUT=$OUTDIR/ecoli_lp_maxEle.cmp.h5
$ CMP_STDOUT=$STDDIR/ecoli_lp_maxEle.cmp.h5
$ METRICS=QualityValue,MergeQV,InsertionQV,DeletionQV,DeletionTag,PulseWidth,SubstitutionQV,SubstitutionTag
$ MAX_ELEMENTS=140000000
$ rm -f $CMP_OUT
$ cp $CMP_IN $CMP_OUT
$ $EXEC $FOFN_IN $CMP_OUT -bymetric -metrics $METRICS -maxElements $MAX_ELEMENTS
[INFO] * [loadPulses] started. (glob)
Either the number of elements exceeds maxElement (140000000). Or the estimated memory
consumption exceeds maxMemory (4 GB).
Loading pulses from .+ by read. (re)
loading 2 alignments for movie 1
loading 2 alignments for movie 2
[INFO] * [loadPulses] ended. (glob)
$ h5diff -c $CMP_OUT $CMP_STDOUT
dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
\d+ differences found (re)
dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
\d+ differences found (re)
dataset: </FileLog/Version> and </FileLog/Version>
\d+ differences found (re)
[1]
#Test loadPulses -byMetric on a multi-streaming job.
$ FOFN_IN=$DATDIR/lambda_bax.fofn
$ CMP_IN=$DATDIR/lambda_bax.cmp.h5
$ CMP_OUT=$OUTDIR/lambda_bax.cmp.h5
$ CMP_STDOUT=$STDDIR/lambda_bax.cmp.h5
$ METRICS=QualityValue,MergeQV,InsertionQV,DeletionQV,DeletionTag,PulseWidth,SubstitutionQV,SubstitutionTag
$ rm -f $CMP_OUT
$ cp $CMP_IN $CMP_OUT
$ $EXEC $FOFN_IN $CMP_OUT -bymetric -metrics $METRICS
[INFO] * [loadPulses] started. (glob)
WARNING: There is insufficient data to compute metric: MergeQV in the file .+ It will be ignored. (re)
loading 2 alignments for movie 1
loading 2 alignments for movie 1
[INFO] * [loadPulses] ended. (glob)
$ h5diff -c $CMP_OUT $CMP_STDOUT
dataset: </FileLog/CommandLine> and </FileLog/CommandLine>
\d+ differences found (re)
dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
\d+ differences found (re)
dataset: </FileLog/Version> and </FileLog/Version>
\d+ differences found (re)
[1]
#Test loadPulses -bymetric for a ccs cmp.h5 file generated from multiple movies.
$ FOFN_IN=$DATDIR/ccs_lp.fofn
$ CMP_IN=$DATDIR/ccs_lp.cmp.h5
$ CMP_OUT=$OUTDIR/ccs_lp.cmp.h5
# The original pls.h5 files disappeared, to use another dataset instead.
$ rm -f CMP_OUT
$ cp $CMP_IN $CMP_OUT
$ $EXEC $FOFN_IN $CMP_OUT -bymetric -metrics QualityValue
[INFO] * [loadPulses] started. (glob)
loading 100 alignments for movie 1
loading 45 alignments for movie 2
[INFO] * [loadPulses] ended. (glob)
$ h5ls -r $CMP_OUT | grep "AlnInfo"
/AlnInfo Group
/AlnInfo/AlnIndex Dataset {145/Inf, 22}
/AlnInfo/NumPasses Dataset {145/Inf}
#Test loadPulses *.fofn cmp.h5 where *.fofn can either contain ccs.h5 or bas.h5
# and the cmp.h5 s readType is CCS
$ CCS_FOFN=$DATDIR/test_ccs.fofn
$ BAS_FOFN=$DATDIR/test_bas.fofn
$ CMP_IN=$DATDIR/test_ccs_bas.cmp.h5
$ CCS_OUT=$OUTDIR/test_ccs_bas_ccs.cmp.h5
$ BAS_OUT=$OUTDIR/test_ccs_bas_bas.cmp.h5
$ cp $CMP_IN $CCS_OUT
$ cp $CMP_IN $BAS_OUT
$ $EXEC $CCS_FOFN $CCS_OUT -metrics QualityValue,DeletionQV,DeletionTag,InsertionQV,SubstitutionQV
[INFO] * [loadPulses] started. (glob)
loading 11 alignments for movie 1
[INFO] * [loadPulses] ended. (glob)
$ sleep 1
$ $EXEC $BAS_FOFN $BAS_OUT -metrics QualityValue,DeletionQV,DeletionTag,InsertionQV,SubstitutionQV
[INFO] * [loadPulses] started. (glob)
loading 11 alignments for movie 1
[INFO] * [loadPulses] ended. (glob)
$ h5diff $CCS_OUT $BAS_OUT
dataset: </FileLog/CommandLine> and </FileLog/CommandLine> (glob)
* differences found (glob)
dataset: </FileLog/Timestamp> and </FileLog/Timestamp>
* differences found (glob)
[1]
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