#!/bin/sh
echo List files without ./ in front
find . | awk '{sub(/.\//," ")}1'


aminosee_do () {
  nice -n $1 aminosee $2 $3 $4 $5 $6 $7 &
  sleep 1
}
aminosee_do_foreground() {
  nice -n $1 aminosee $2 $3 $4 $5 $6 $7
}

parallel_peptides () {
  echo "                                         =///"
  echo "-------------------------------------------"
  echo STARTING PARALLEL DECODE FOR $1 $2 $3
  echo "-------------------------------------------"
  echo "                                         =///"
  aminosee_do            1 $1 $2 0 $1 $2 $3 $4 &
  aminosee_do_foreground 1 $1 $2 $3 $4 --peptide=Ochre
  aminosee_do            2 $1 $2 $3 $4 --peptide=Glutamic_acid
  aminosee_do_foreground 3 $1 $2 $3 $4 --peptide=Aspartic_acid
  aminosee_do            4 $1 $2 $3 $4 --peptide=Amber
  aminosee_do_foreground 5 $1 $2 $3 $4 --peptide=Cysteine
  aminosee_do            6 $1 $2 $3 $4 --peptide=Glycine
  aminosee_do_foreground 7 $1 $2 $3 $4 --peptide=Alanine

  aminosee_do            1 $1 $2 $3 $4 --peptide=Methionine
  aminosee_do            2 $1 $2 $3 $4 --peptide=Valine
  aminosee_do_foreground 3 $1 $2 $3 $4 --peptide=Leucine
  aminosee_do            4 $1 $2 $3 $4 --peptide=Isoleucine
  aminosee_do_foreground 5 $1 $2 $3 $4 --peptide=Phenylalanine
  aminosee_do            6 $1 $2 $3 $4 --peptide=Tryptophan
  aminosee_do            7 $1 $2 $3 $4 --peptide=Serine
  aminosee_do_foreground 8 $1 $2 $3 $4 --peptide=Threonine

  aminosee_do            1 $1 $2 $3 $4 --peptide=Opal
  aminosee_do_foreground 2 $1 $2 $3 $4 --peptide=Glutamine
  aminosee_do            3 $1 $2 $3 $4 --peptide=Asparagine
  aminosee_do_foreground 4 $1 $2 $3 $4 --peptide=Tyrosine
  aminosee_do            5 $1 $2 $3 $4 --peptide=Arginine
  aminosee_do_foreground 6 $1 $2 $3 $4 --peptide=Lysine
  aminosee_do_foreground 7 $1 $2 $3 $4 --peptide=Histidine

  echo "                                         =///"
  echo "-------------------------------------------"
  echo FINISHED PARALLEL DECODE FOR $1
  echo "-------------------------------------------"
  echo "                                         =///"
}
#
# parallel_peptides Brown_Kiwi_NW_013982187v1.fa $1 $2 $3
# parallel_peptides Caenorhabditis_elegans-WBcel235-dna-chromosome-V.fa $1 $2 $3
# parallel_peptides Human-GRCh38.p12_chr2.gbk $1 $2 $3
# parallel_peptides Human-GRCh38.p12_chr2.fa $1 $2 $3
# parallel_peptides Caenorhabditis_elegans.WBcel235.dna_sm.toplevel.fa $1 $2 $3
# parallel_peptides Chimp_Clint_chrY.gb $1 $2 $3
# parallel_peptides Octopus_Bimaculoides_v2_0_chrUn.fa $1 $2 $3
# parallel_peptides chrY Pan troglodytes C0471 Clint.gbk $1 $2 $3
# parallel_peptides homo-sapien-hs_ref_GRCh38.p12_chr2.fa $1 $2 $3

if [ $(uname)=Darwin ]; then
  echo macos
  find -f *.fa *.mfa *.gbk *.txt
  sleep 2
  find -f *.fa *.mfa *.gbk *.txt -exec ./batch-peptides.sh {} $1 $2 $3 $4 $5 $6 $7   \;
fi

if [ $(uname)=Linux ]; then
  echo linux
  find *.fa *.mfa *.gbk *.txt
  sleep 2
  find *.fa *.mfa *.gbk *.txt -exec ./batch-peptides.sh {} $1 $2 $3 $4 $5 $6 $7   \;
fi


echo "FINISHED ALL OF PROCESSS SCRIPT - FAROUT"