#!/bin/bash

############################################################################
# Copyright (c) 2015 Saint Petersburg State University
# Copyright (c) 2011-2014 Saint Petersburg Academic University
# All Rights Reserved
# See file LICENSE for details.
############################################################################

mkdir tmp

for i in $*
do
  cp $i tmp
done
gzip -d tmp/*
mkdir tmp/mixed
if [ -e "tmp/*left.corrected*.fastq" ]
then
  perl shuffleSequences_fastq.pl tmp/*left.corrected*.fastq tmp/*right.corrected*.fastq tmp/mixed/mixed.fastq
  rm tmp/*corrected*.fastq
elif [ -e "tmp/*left.corrected*.fasta" ]
then
  perl shuffleSequences_fasta.pl tmp/*left.corrected*.fasta tmp/*right.corrected*.fastq tmp/mixed/mixed.fasta
  rm tmp/*corrected*.fasta

elif [ -e "tmp/*_1.fastq" ]
then
  echo "here"
  perl shuffleSequences_fastq.pl tmp/*_1.fastq tmp/*_2.fastq tmp/mixed/mixed.fastq
  rm tmp/*_1.fastq
  rm tmp/*_2.fastq
elif [ -e "tmp/*_1.fasta" ]
then
  perl shuffleSequences_fasta.pl tmp/*_1.fasta tmp/*_2.fasta tmp/mixed/mixed.fasta
  rm tmp/*_1.fasta
  rm tmp/*_2.fasta
fi
velvethrun="velveth results 55"
if [ -e "tmp/mixed/mixed.fasta" ] 
then
  let "velvethrun += " -shortPaired -fasta tmp/mixed/mixed.fasta""
elif [ -e "tmp/mixed/mixed.fastq" ] 
then 
  let "velvethrun += " -shortPaired -fastq tmp/mixed/mixed.fastq""
fi
#for filename in tmp/; 
FOUND=0

echo $velvethrun
cd tmp/

for filename in *.fasta        # Перебор всех файлов в текущем каталоге.
do
echo $filename
if [ -e $filename ]
then
velvethrun="$velvethrun -short -fasta tmp/$filename"
fi
done
for filename in *.fastq        # Перебор всех файлов в текущем каталоге.
do
echo $filename
if [ -e $filename ]
then
velvethrun="$velvethrun -short -fastq tmp/$filename"
fi
done
cd ../
echo $velvethrun
./$velvethrun
./velvetg results -exp_cov auto -cov_cutoff auto -scaffolding no
rm tmp -rf

#perl shuffleSequences_fastq.pl tmp/*_1*.fastq tmp/*_2*.fastq tmp/mixed.fastq