test/cmdlinetest_narrowpeak_pe

   1 #!/bin/bash
   2
   3 # integrative subcmds testing
   4
   5 if [ $# -lt 1 ];then
   6     echo "Run all tests for subcommands of MACS2. Need 1 parameter for a tag name! A unique string combining date, time and MACS2 version is recommended. ./test.sh <TAG>"
   7     exit
   8 fi
   9
  10 # test all sub-commands
  11 TAG=$1
  12
  13 CHIP=CTCF_SE_ChIP_chr22_50k.bed.gz
  14 CTRL=CTCF_SE_CTRL_chr22_50k.bed.gz
  15
  16 CHIPPE=CTCF_PE_ChIP_chr22_50k.bam
  17 CTRLPE=CTCF_PE_CTRL_chr22_50k.bam
  18
  19 CHIPBEDPE=CTCF_PE_ChIP_chr22_50k.bedpe.gz
  20 CTRLBEDPE=CTCF_PE_CTRL_chr22_50k.bedpe.gz
  21
  22 CHIPCONTIGS50K=contigs50k.bed.gz
  23
  24 CHIPBIGSPEEDTEST=CTCF_12878_5M.bed.gz
  25 CTRLBIGSPEEDTEST=input_12878_5M.bed.gz
  26
  27 # callpeak
  28 echo "1. callpeak"
  29
  30 mkdir ${TAG}_run_callpeak_pe_narrow
  31 mkdir ${TAG}_run_callpeak_narrow
  32
  33 macs2 callpeak -g 52000000 -t $CHIP -c $CTRL -n run_callpeak_narrow0 -B --outdir ${TAG}_run_callpeak_narrow --cutoff-analysis &> ${TAG}_run_callpeak_narrow/run_callpeak_narrow0.log
  34
  35 cat ${TAG}_run_callpeak_narrow/run_callpeak_narrow0.log
  36
  37 macs2 callpeak -g 52000000 -f BAMPE -t $CHIPPE -c $CTRLPE -n run_callpeak_bampe_narrow -B --outdir ${TAG}_run_callpeak_pe_narrow --call-summits --verbose 3 &> ${TAG}_run_callpeak_pe_narrow/run_callpeak_bampe_narrow.log
  38
  39 cat ${TAG}_run_callpeak_pe_narrow/run_callpeak_bampe_narrow.log
  40
  41 echo "2. search for errors or warnings in log files"
  42 flag=0
  43 for i in `ls ${TAG}_run_*/*.log`;do
  44     echo " checking $i..."
  45     egrep -A 2 -B 2 -i "error|warning" $i;
  46     if [[ $? == 0 ]];then
  47         echo " ... error/warning found!"
  48         let "flag=1";
  49     else
  50         echo " ... clear!"
  51     fi
  52 done;
  53
  54 if [[ $flag == 1 ]]; then
  55     echo " Error or Warning can be found! Quit the test!"
  56     exit 1;
  57 fi
  58
  59 echo "3. compare with standard outputs"
  60
  61 flag=0
  62 # we do not check the consistency of random subsampling results
  63 subfolders=(callpeak_pe_narrow callpeak_narrow)
  64
  65 m=0
  66 n=0
  67 for i in ${subfolders[@]};do
  68     let "m+=1"
  69     let "n=0"
  70     for j in `ls standard_results_${i}/*`; do
  71         k=`basename $j`
  72         let "n+=1"
  73         echo "14.${m}.${n} checking $i $k ..."
  74         fq=${TAG}_run_${i}/${k}
  75         fs=standard_results_${i}/${k}
  76         if [ ! -f "$fq" ]; then
  77             continue
  78         fi
  79         sort $fq > tmp_fq.txt
  80         sort $fs > tmp_fs.txt
  81         d=`diff tmp_fq.txt tmp_fs.txt`
  82         if [ -z "$d" ]; then
  83             echo " ... success!"
  84         else
  85             echo " ... failed! Difference:"
  86             diff tmp_fq.txt tmp_fs.txt | head -10
  87             let "flag=1";
  88         fi
  89     done
  90 done
  91 rm -f tmp_fq.txt tmp_fs.txt
  92
  93 # exit with 1 if test fails
  94 if [ $flag -eq 1 ];then
  95     exit $flag;
  96 fi
  97
  98 # END of test