Test basic mode of ipdSummary.py.

  $ . $TESTDIR/portability.sh

Load in data:

  $ DATA=$TESTDIR/../data
  $ INPUT=$DATA/p4-c2-lambda-mod-decode.cmp.h5
  $ REFERENCE=$DATA/lambda/sequence/lambda.fasta

Run basic ipdSummary.py:

  $ ipdSummary.py --pvalue 0.001 --numWorkers 1 --methylFraction --identify m6A,m4C --csv tmp.csv --gff tmp.gff --summary_h5 tmp.h5 --reference $REFERENCE $INPUT

Look at output csv file:

  $ head -3 tmp.csv
  refName,tpl,strand,base,score,tMean,tErr,modelPrediction,ipdRatio,coverage,frac,fracLow,fracUp
  "lambda_NEB3011",13190,0,A,3,1.119,0.096,1.125,0.995,3,,,
  "lambda_NEB3011",13190,1,T,2,0.952,0.256,1.126,0.846,3,,,

  $ grep 14756 tmp.csv
  "lambda_NEB3011",14756,0,G,0,0.209,0.030,0.288,0.726,164,,,
  "lambda_NEB3011",14756,1,C,23,0.692,0.049,0.519,1.333,165,0.370,0.154,0.614

Look at output gff file:

  $ sed 's/\t/ /g' tmp.gff
  ##gff-version 3
  ##source ipdSummary.py v2.0
  ##source-commandline /home/UNIXHOME/dalexander/.virtualenvs/VE/bin/ipdSummary.py --pvalue 0.001 --numWorkers 1 --methylFraction --identify m6A,m4C --csv tmp.csv --gff tmp.gff --summary_h5 tmp.h5 --reference /home/UNIXHOME/dalexander/Projects/software/smrtanalysis/bioinformatics/tools/kineticsTools/test/cram/../data/lambda/sequence/lambda.fasta /home/UNIXHOME/dalexander/Projects/software/smrtanalysis/bioinformatics/tools/kineticsTools/test/cram/../data/p4-c2-lambda-mod-decode.cmp.h5
  ##sequence-region ref000001 1 48502
  lambda_NEB3011 kinModCall modified_base 14060 14060 31 - . coverage=49;context=ACGTTATTGCGGAACTTACAACCGCTCAGGCATTTGCTGCA;IPDRatio=2.16
  lambda_NEB3011 kinModCall modified_base 14657 14657 35 + . coverage=155;context=CGGCACAGCCGGGCGATGTGCTGCTGTGCTGTTTTGGTTCA;IPDRatio=1.56
  lambda_NEB3011 kinModCall modified_base 14743 14743 32 - . coverage=173;context=TACCTCTCTCGTTTGCTCAGTTGTTCAGGAATATGGTGCAG;IPDRatio=1.51
  lambda_NEB3011 kinModCall m4C 14756 14756 23 - . coverage=165;context=CCATTTGTCGGTGTACCTCTCTCGTTTGCTCAGTTGTTCAG;IPDRatio=1.33;frac=0.370;fracLow=0.154;fracUp=0.614;identificationQv=25
  lambda_NEB3011 kinModCall modified_base 14769 14769 32 - . coverage=168;context=GTGTGCGTCGCTGCCATTTGTCGGTGTACCTCTCTCGTTTG;IPDRatio=1.57
  lambda_NEB3011 kinModCall modified_base 14800 14800 34 - . coverage=173;context=GCGCGCCATGCCCGGTGACGCCAGAGGGAGTGTGTGCGTCG;IPDRatio=1.70
  lambda_NEB3011 kinModCall modified_base 14831 14831 33 + . coverage=161;context=CATGGCGCGCATCTGCCTTTACGGGGATTTACAACGATTTG;IPDRatio=1.57
  lambda_NEB3011 kinModCall modified_base 14834 14834 31 + . coverage=166;context=GGCGCGCATCTGCCTTTACGGGGATTTACAACGATTTGGTC;IPDRatio=1.69
  lambda_NEB3011 kinModCall modified_base 14841 14841 32 + . coverage=162;context=ATCTGCCTTTACGGGGATTTACAACGATTTGGTCGCCGCAT;IPDRatio=1.58
  lambda_NEB3011 kinModCall modified_base 14847 14847 35 - . coverage=172;context=AGGTCGATGCGGCGACCAAATCGTTGTAAATCCCCGTAAAG;IPDRatio=1.86
  lambda_NEB3011 kinModCall modified_base 14864 14864 46 - . coverage=166;context=CCCCCGTTTTCACACGAAGGTCGATGCGGCGACCAAATCGT;IPDRatio=1.71
  lambda_NEB3011 kinModCall m4C 14884 14884 30 - . coverage=173;context=CAGTGCCCGGATGGCTTCAGCCCCCGTTTTCACACGAAGGT;IPDRatio=2.18;frac=0.313;fracLow=0.169;fracUp=0.450;identificationQv=19
  lambda_NEB3011 kinModCall modified_base 14909 14909 35 + . coverage=162;context=AGCCATCCGGGCACTGGCCACACAGCTCCCGGCGTTTCGTC;IPDRatio=1.77
  lambda_NEB3011 kinModCall m6A 14983 14983 210 + . coverage=160;context=TTGCCGGGCGGGACGTCAGCACGTCCGGGTTAACGGCGCAG;IPDRatio=6.76;frac=0.982;fracLow=0.883;fracUp=0.992;identificationQv=194
  lambda_NEB3011 kinModCall m6A 14992 14992 208 - . coverage=162;context=CTCATGTAACTGCGCCGTTAACCCGGACGTGCTGACGTCCC;IPDRatio=6.67;frac=0.854;fracLow=0.723;fracUp=0.934;identificationQv=194
  lambda_NEB3011 kinModCall m4C 14997 14997 61 - . coverage=140;context=AGAGTCTCATGTAACTGCGCCGTTAACCCGGACGTGCTGAC;IPDRatio=2.35;frac=0.475;fracLow=0.080;fracUp=0.877;identificationQv=21
  lambda_NEB3011 kinModCall m4C 14998 14998 23 - . coverage=172;context=CAGAGTCTCATGTAACTGCGCCGTTAACCCGGACGTGCTGA;IPDRatio=1.53;frac=0.336;fracLow=0.097;fracUp=0.553;identificationQv=48
  lambda_NEB3011 kinModCall modified_base 15008 15008 47 + . coverage=162;context=CGGGTTAACGGCGCAGTTACATGAGACTCTGCCTGATGGCG;IPDRatio=1.73
  lambda_NEB3011 kinModCall modified_base 15039 15039 51 - . coverage=169;context=CCGGCGACTCTGGGAACAATATGAATTACAGCGCCATCAGG;IPDRatio=1.83
  lambda_NEB3011 kinModCall m6A 15041 15041 28 - . coverage=161;context=CCCCGGCGACTCTGGGAACAATATGAATTACAGCGCCATCA;IPDRatio=1.52;frac=0.207;fracLow=0.070;fracUp=0.355;identificationQv=4
  lambda_NEB3011 kinModCall modified_base 15066 15066 37 + . coverage=161;context=CCCAGAGTCGCCGGGGCCAAGTCAGGTGGCGTATTCCAGAT;IPDRatio=1.68
  lambda_NEB3011 kinModCall modified_base 15074 15074 33 - . coverage=171;context=CCAGGACAATCTGGAATACGCCACCTGACTTGGCCCCGGCG;IPDRatio=1.79
  lambda_NEB3011 kinModCall modified_base 15078 15078 33 - . coverage=168;context=GCCCCCAGGACAATCTGGAATACGCCACCTGACTTGGCCCC;IPDRatio=1.61
  lambda_NEB3011 kinModCall modified_base 15089 15089 32 - . coverage=167;context=CAATGGCGGCAGCCCCCAGGACAATCTGGAATACGCCACCT;IPDRatio=1.56
  lambda_NEB3011 kinModCall modified_base 15095 15095 33 - . coverage=167;context=ATCCGGCAATGGCGGCAGCCCCCAGGACAATCTGGAATACG;IPDRatio=1.59
  lambda_NEB3011 kinModCall modified_base 15118 15118 32 - . coverage=163;context=GGTGGCTCCGGCGGTAAAGAATGATCCGGCAATGGCGGCAG;IPDRatio=1.54
  lambda_NEB3011 kinModCall modified_base 15121 15121 31 - . coverage=149;context=AAGGGTGGCTCCGGCGGTAAAGAATGATCCGGCAATGGCGG;IPDRatio=1.58
  lambda_NEB3011 kinModCall modified_base 15124 15124 35 - . coverage=170;context=TGCAAGGGTGGCTCCGGCGGTAAAGAATGATCCGGCAATGG;IPDRatio=1.57
  lambda_NEB3011 kinModCall modified_base 15195 15195 33 - . coverage=164;context=AGCACCATACTGGCACCGAGAGAAAACAGGATGCCGGTCAT;IPDRatio=1.60
  lambda_NEB3011 kinModCall modified_base 15239 15239 33 + . coverage=157;context=TGGTGTGGCGCAGATGCTGGCACCGAAAGCCAGAACTCCCC;IPDRatio=1.64
  lambda_NEB3011 kinModCall modified_base 15261 15261 38 - . coverage=167;context=CCGTTATCCGTTGTCTGTATACGGGGAGTTCTGGCTTTCGG;IPDRatio=1.73
  lambda_NEB3011 kinModCall modified_base 15291 15291 31 + . coverage=158;context=ACGGATAACGGTAAGCAGAACACCTATTTCTCCTCACTGGA;IPDRatio=1.67
  lambda_NEB3011 kinModCall modified_base 15292 15292 41 - . coverage=166;context=ATCCAGTGAGGAGAAATAGGTGTTCTGCTTACCGTTATCCG;IPDRatio=1.61
  lambda_NEB3011 kinModCall m6A 15381 15381 21 - . coverage=169;context=GCCGTGCTGATCTCCTGAGAAACCACGCGTGACCCCACGCG;IPDRatio=1.41;frac=0.170;fracLow=0.086;fracUp=0.242;identificationQv=13
  lambda_NEB3011 kinModCall modified_base 15402 15402 33 - . coverage=169;context=TGACCACCGTCCCCTTCGTCTGCCGTGCTGATCTCCTGAGA;IPDRatio=1.48
  lambda_NEB3011 kinModCall m4C 15439 15439 30 + . coverage=164;context=GTCAGGTTGTGGTGATTGGTCGCTGATGCAAAATGTTTTAT;IPDRatio=1.57;frac=0.627;fracLow=0.346;fracUp=0.896;identificationQv=3
  lambda_NEB3011 kinModCall modified_base 15566 15566 31 + . coverage=118;context=GAAGGACAACCTGAAGTCCACGCAGTTGCTGAGTGTGATCG;IPDRatio=1.78
  lambda_NEB3011 kinModCall m6A 16380 16380 21 - . coverage=10;context=CATTTATCCACATCCGCCGCACCAAGACGTTTCCCCATGCC;IPDRatio=6.05;identificationQv=5
  lambda_NEB3011 kinModCall m6A 16658 16658 21 - . coverage=6;context=GGGCGCTGAAGCTGTAGCGGAACGGCGCGCCATCATCCGGC;IPDRatio=2.78;identificationQv=21

What about the H5 file?

  $ h5ls -r tmp.h5
  /                        Group
  /ref000001               Dataset {48502}