BioInfo/BS-Seq/bwa-meth/example/test.sh

   1 # from http://tldp.org/LDP/abs/html/debugging.html#ASSERT
   2 set -e -o nounset
   3 assert ()                 #  If condition false,
   4 {                         #+ exit from script
   5                           #+ with appropriate error message.
   6   E_PARAM_ERR=98
   7   E_ASSERT_FAILED=99
   8
   9
  10   if [ -z "$2" ]          #  Not enough parameters passed
  11   then                    #+ to assert() function.
  12     return $E_PARAM_ERR   #  No damage done.
  13   fi
  14
  15   lineno=$2
  16
  17   if [ ! $1 ]
  18   then
  19     echo "Assertion failed:  \"$1\""
  20     echo "File \"$0\", line $lineno"    # Give name of file and line number.
  21     exit $E_ASSERT_FAILED
  22   # else
  23   #   return
  24   #   and continue executing the script.
  25   fi
  26   echo "
  27 [TEST]: '$1' PASSED at line:$lineno
  28 "
  29 }
  30
  31
  32 rm -f ref.bwameth* bwa-meth.bam
  33
  34 python ../bwameth.py index ref.fa
  35
  36 ##########################
  37 # test read-group
  38 ##########################
  39 rm -f bwa-meth.bam*
  40 python ../bwameth.py --read-group $'@RG\tID:asdf\tSM:asdf' --reference ref.fa t_R1.fastq.gz t_R2.fastq.gz | samtools view -b - > bwa-meth.bam
  41
  42 n=`samtools view -H bwa-meth.bam | grep "@RG" | grep -cw "ID:asdf"`
  43 assert "$n -eq 1" $LINENO
  44 a=`samtools view  bwa-meth.bam | grep -c RG:Z:asdf`
  45 b=`samtools view  bwa-meth.bam  | wc -l`
  46 assert "$a -eq $b" $LINENO
  47
  48
  49
  50 ##########################
  51 # test normal alignment
  52 ##########################
  53 python ../bwameth.py --reference ref.fa t_R1.fastq.gz t_R2.fastq.gz \
  54         | samtools view -b - > bwa-meth.bam
  55 assert " -e bwa-meth.bam " $LINENO
  56
  57 ##########################
  58 # test multiple fastq sets
  59 ##########################
  60 # NOTE: here we repeat the same fastq, but you'd want diff ones from same sample
  61 rm -f bwa-meth.bam*
  62 python ../bwameth.py --reference ref.fa t_R1.fastq.gz,t_R1.fastq.gz t_R2.fastq.gz,t_R2.fastq.gz \
  63         | samtools view -b - > bwa-meth.bam
  64 assert " -e bwa-meth.bam " $LINENO
  65
  66 ##########################
  67 # test single end
  68 ##########################
  69 rm -f bwa-meth.bam*
  70 python ../bwameth.py --reference ref.fa t_R1.fastq.gz \
  71         | samtools view -b - > bwa-meth.bam
  72
  73 assert " -e bwa-meth.bam " $LINENO
  74 count=`samtools view -cf2 bwa-meth.bam`
  75 assert "$count -eq 0" $LINENO
  76 count=`samtools view -cF4 bwa-meth.bam`
  77 assert "$count -gt 1000" $LINENO
  78
  79
  80 ##############################
  81 # test single end, many fastqs
  82 ##############################
  83 rm -f bwa-meth.bam*
  84 python ../bwameth.py --reference ref.fa t_R1.fastq.gz,t_R1.fastq.gz \
  85         | samtools view -b - > bwa-meth.bam
  86 assert " -e bwa-meth.bam " $LINENO
  87 count2=`samtools view -cf2 bwa-meth.bam`
  88 assert "$count2 -eq 0" $LINENO
  89 count2=`samtools view -cF4 bwa-meth.bam`
  90 assert "$count2 -gt $count" $LINENO
  91
  92
  93 echo "Success: ALL Tests PASS"