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run_mummer4.sh [2018/07/03 16:26] (current)
hyjeong created
Line 1: Line 1:
 +====== run-mummer4.sh ======
  
 +  #!/bin/sh
 +  #
 +  # run-mummer4.sh:​ MUMmer-based shell script for aligning draft sequences to a 
 +  #                 ​finished genome. ​
 +  #
 +  ​
 +  if [ $# = 0 ]
 +      then 
 +          echo "Usage : run-mummer4.sh <​prefix>​ <​ref_seq_file>​ <​query_seq_file>​ [-q]" 1>&2
 +          echo "The last option is for delta-filter."​
 +          echo "Other nucmer default options: -maxmatch -c 100"
 +            exit 1
 +  fi
 +  ​
 +  #nucmer --prefix=$1 -mum -c 100 $2 $3
 +  nucmer --prefix=$1 -mum -c 1000 $2 $3
 +  ​
 +  if [ "​$4"​ = "​-q"​ ] 
 +      then
 +          delta-filter $4 $1.delta > tmp
 +          mv $1.delta $1.delta.org
 +          mv tmp $1.delta
 +  fi
 +  ​
 +  show-coords -rcl $1.delta > $1.coords
 +  ​
 +  REFNAME=`awk '​$1~/​^>/​{print $1}' $2 | sed '​s/​^>//'​`
 +  ​
 +  for QRYNAME in `awk '​$1~/​^>/​{print $1}' $3 | sed '​s/​^>//'​`
 +  do
 +      show-aligns $1.delta $REFNAME $QRYNAME > $1.aligns
 +  done
 +  ​
 +  mummerplot --postscript $1.delta -R $2 -Q $3  --layout --prefix=$1
run_mummer4.sh.txt ยท Last modified: 2018/07/03 16:26 by hyjeong