2c1d15c2278d48af89dd575bdb47448dee5f729e

@ -5,6 +5,13 @@

export AwkCmd="gawk"

# setup the LC_ALL environment variable (for Linux mostly)
# so the GNU tools (like sort) will work properly
  
export LANG=C
export LC_ALL=C


########################
#
# General usage functions
@ -96,6 +103,16 @@ function seqlength {
  $AwkCmd -v t="`head -1 $1 | wc -c`" '{print $3 - t - $1 + 1}'
}

function readfirstfastaseq {
	awk '(/^>/ && first) {on=0}
	     (on) {seq=seq $1}
	     (/^>/ && ! first) { first = 1
	                         on = 1
	                       } 
	     END {print seq}
	    ' $*
}

# extract a subseq from a fasta sequence
# 	- $1 : The fasta file to cut
#   - $2 : First position of the subsequence (first position is numered 1), 
@ -141,6 +158,54 @@ function formatfasta {
								END    { printfasta(seq)}' "${1}"
}

# Reverse complement a DNA string 
#    - $1 : The DNA string to reverse complement
function reversecomp {
	echo $1 \
	| tr 'Aa' '@!' | tr 'Tt' 'Aa' | tr '@!' 'Tt' \
	| tr 'Cc' '@!' | tr 'Gg' 'Cc' | tr '@!' 'Gc' \
	| tr 'Mm' '@!' | tr 'Kk' 'Mm' | tr '@!' 'Kk' \
	| tr 'Rr' '@!' | tr 'Yy' 'Rr' | tr '@!' 'Yy' \
	| tr 'Ww' '@!' | tr 'Ss' 'Ww' | tr '@!' 'Ss' \
	| tr 'Bb' '@!' | tr 'Vv' 'Bb' | tr '@!' 'Vv' \
	| tr 'Dd' '@!' | tr 'Hh' 'Dd' | tr '@!' 'Hh' \
	| rev
}

#
# Process management related function
#

function timeoutcmd() {
  local seconde=$1
  shift

  $* &

  local mainpid=$!
  sleep $seconde &
  local sleeppid=$!

  local nproc=$(ps $mainpid $sleeppid | tail -n +2 | wc -l)

  while (( nproc > 1 )) ; do
    sleep 1
    nproc=$(ps $mainpid $sleeppid | tail -n +2 | wc -l)
  done

  local timealive=$(ps $sleeppid | tail -n +2 | wc -l)

  if (( timealive > 0 )) ; then
    kill -9 $sleeppid
  else
        if (( $(ps $mainpid | tail -n +2 | wc -l) > 0 )) ; then
                kill -9 $mainpid
        logwarning "Timeout after ${seconde}s on command : $*"
                return 1
        fi
  fi
}


#
#