# rnaseq denovo

#!/bin/bash

# input - diretório contendo os arquivos de entrada no formato .fastq
input=$1

# validação do parâmetro "input"
if [ ! ${input} ]
then
echo "Missing input directory"
exit
else
if [ ! -d ${input} ]
then
echo "Wrong input directory ${input}"
exit
fi
fi

# output - diretório para armazenar o resultado do processo de montagem
output=$2

# validação do parâmetro "output"
if [ ! ${output} ]
then
echo "Missing output directory"
exit
else
if [ ! -d ${output} ]
then
echo "Wrong output directory ${output}"
exit
fi
fi

num_threads="8"
mem_gb="10G"

###
# Arquivos e diretórios de saída (output)
#

basedir_out="${output}/"

renamed_out="${basedir_out}/renamed"

trinity_out="${basedir_out}/trinity_assembled"

mkdir -p ${renamed_out}

left=()
left_singleton=()

right=()
right_singleton=()

echo "Renaming step ..."

mkdir -p ${trinity_out}

for fastq in `ls ${input}/*.fastq`; do
# obtendo nome do arquivo
fastqbn=`basename ${fastq}`;
if [[ ! $fastqbn =~ \.bad_ ]]; then
renamed_fastq="${renamed_out}/${fastqbn}"
if [ ! -e ${renamed_fastq} ]; then
echo -e "\tRenaming ${fastqbn} ..."
if [[ ${fastqbn} =~ _1[\._] ]]; then
awk '{ if (NR%4==1) { if ($1!~/\/1$/) { print $1"/1" } else { print $0 } } else if (NR%4==3) { print "+" } else { print $0 } }' ${fastq} > ${renamed_fastq}
elif [[ ${fastqbn} =~ _2[\._] ]]; then
awk '{ if (NR%4==1) { if ($1!~/\/2$/) { print $1"/2" } else { print $0 } } else if (NR%4==3) { print "+" } else { print $0 } }' ${fastq} > ${renamed_fastq}
else
echo "Warning: ${fastqbn} discarded!"
fi
fi

if [[ ${fastqbn} =~ _1[\._] ]]; then
if [[ ${fastqbn} =~ singletons ]]; then
left_singleton=($(printf "%s\n" ${left_singleton[@]} ${renamed_fastq} | sort -u ))
else
left=($(printf "%s\n" ${left[@]} ${renamed_fastq} | sort -u ))
fi
elif [[ ${fastqbn} =~ _2[\._] ]]; then
if [[ ${fastqbn} =~ singleton ]]; then
right_singleton=($(printf "%s\n" ${right_singleton[@]} ${renamed_fastq} | sort -u ))
else
right=($(printf "%s\n" ${right[@]} ${renamed_fastq} | sort -u ))
fi
else
echo "Warning: ${fastqbn} discarded!"
fi
fi
done

if [ ! -d ${trinity_out}/Trinity.timing ]; then

echo -e "Assembling step (Trinity) ..."

Trinity --KMER_SIZE 27 \
--output ${trinity_out} \
--seqType fq \
--max_memory ${mem_gb} \
--CPU ${num_threads} \
--min_per_id_same_path 95 \
--max_diffs_same_path 5 \
--path_reinforcement_distance 5 \
--group_pairs_distance 500 \
--min_glue 5 \
--min_contig_length 600 \
--min_kmer_cov 3 \
--left $(IFS=, ; echo "${left[*]},${left_singleton[*]}") \
--right $(IFS=, ; echo "${right[*]},${right_singleton[*]}") \
> ${trinity_out}/Trinity.log.out.txt \
2> ${trinity_out}/Trinity.log.err.txt
fi