view runLinkYX.sh @ 13:ef5c8ed727b0

toolshed12

#!/bin/bash
set -e; mkdir -p vcf; mkdir -p bam; mkdir -p references; mkdir -p scripts;

email_address_of_user=$1;
name_of_user_computer=$2;

#read config variables
echo "Reading config...." >&2
#echo `ls -l`
computer_name=`hostname`;
if [ $computer_name == $name_of_user_computer ]; then
	#local_computer
	source config_devel;
else 
	#metacentrum machine
	source config_meta;
fi

#initally we believe that all files are present
ok=true;

#we get to know if files are provided and if they are in .fasta or .fastq format
#first, rename files to shorter versions (fastq->fq, fasta->fa)
rename 's/fasta$/fa/' input/*.fasta 2>/dev/null
rename 's/fastq$/fq/' input/*.fastq 2>/dev/null

check_if_exists () 
{
for ARG in "$@";
    do
	if [[ -e "input/${ARG}_1.fq" ]]; then
		eval ${ARG}_ext=fq
	elif [[ -e "input/${ARG}_1.fa" ]]; then
		eval ${ARG}_ext=fa
	else
		ok=false;
	fi
    done;
}

check_if_paired_end ()
{
for ARG in "$@";
    do
	extension=$(eval "echo \$${ARG}_ext"); #echo $extension;
      
	if [[ (-e "input/${ARG}_1.${extension}") && (-e "input/${ARG}_2.${extension}") ]]; then
		eval ${ARG}_paired=paired;
	else
		eval ${ARG}_paired=single;
	fi
    done;
}

#check if file with reads exist
check_if_exists mother father daughter son;
#and determine whether they are single or paired-end reads
check_if_paired_end  mother father daughter son;

if [ $ok == true ]; then
	echo "mother reads names:" $mother_ext $mother_paired;
	echo "father reads names:" $father_ext $father_paired;
	echo "daughter reads names:" $daughter_ext $daughter_paired;
	echo "son reads names:" $son_ext $son_paired;

if [[ $father_ext =~ (fq) ]] && [[ $son_ext =~ (fq) ]]; then
		#no conversion needed, both fastq files
		male_ext=fq;
else
		#convert to fasta (we need to merge father and son reads in order to build male reference contigs)
		#father OR son is fasta
		echo "converting..";
		male_ext=fa;
		
		if [[ father_1.$father_ext =~ (fq) ]]; then
		#father is fastq and must be converted to fasta
		  fastq_to_fasta -n -Q33 -i input/father_1.$father_ext -o input/father_1.$male_ext;
		  fastq_to_fasta -n -Q33 -i input/father_2.$father_ext -o input/father_2.$male_ext;
		  father_ext=fa;
		
		else 
		#son is fastq and must be converted to fasta
		  fastq_to_fasta -n -Q33 -i input/son_1.$father_ext -o input/son_1.$male_ext;
		  fastq_to_fasta -n -Q33 -i input/son_2.$father_ext -o input/son_2.$male_ext;
		  son_ext=fa;
		fi
fi
		#merging of father and son files
		echo "concatenating..";
		  cat input/father_1.$father_ext input/son_1.$son_ext >input/father_and_sons_1.$male_ext;
		
		if [[ $father_paired =~ (paired) ]] && [[ $son_paired =~ (paired) ]]; then
		  cat input/father_2.$father_ext input/son_2.$son_ext >input/father_and_sons_2.$male_ext;
		fi
	
	
	#NOW run Trinity to assemble mother contigs
	#in: mother reads out: reference.fasta
	PBS_NUM_PPN_used=$(($PBS_NUM_PPN_used - 2));
	echo "processors used:" $PBS_NUM_PPN_used;

#<<PREVENT_TRINITY_MOTHER
	#assemble mother reads in single or paired-end mode
	if [[ $mother_paired =~ (paired) ]]; then
	    $trinity --CPU $PBS_NUM_PPN_used --seqType $mother_ext --JM 20G --left input/mother_1.$mother_ext --right input/mother_2.$mother_ext --output trinity_out_dir_mother 1>$trinity_stdout 2>&1
	    echo "$trinity --CPU $PBS_NUM_PPN_used --seqType $mother_ext --JM 20G --left input/mother_1.$mother_ext --right input/mother_2.$mother_ext --output trinity_out_dir_mother 1>$trinity_stdout 2>&1";
	else
	    $trinity --CPU $PBS_NUM_PPN_used --seqType $mother_ext --JM 20G --single input/mother_1.$mother_ext --output trinity_out_dir_mother 1>$trinity_stdout 2>&1
	    echo "$trinity --CPU $PBS_NUM_PPN_used --seqType $mother_ext --JM 20G --single input/mother_1.$mother_ext --output trinity_out_dir_mother 1>$trinity_stdout 2>&1";
	fi

	#retrieve assembled contigs and name them as reference.fasta
	mv trinity_out_dir_mother/Trinity.fasta reference_pro.fasta
	perl -pe 's/(>[\S]+).+/$1/' reference_pro.fasta >references/reference.fasta; rm reference_pro.fasta;
#PREVENT_TRINITY_MOTHER

	grep ">" references/reference.fasta | sed 's/>//g' >references/reference_contig_names

	#now call to_get_vcf_files.sh to map reads to reference contigs
	./scripts/to_get_vcf_files.sh references/reference.fasta mother_1.$mother_ext mother_2.$mother_ext mother $mother_paired
	echo "Mother mapping successful.";
	./scripts/to_get_vcf_files.sh references/reference.fasta father_1.$mother_ext father_2.$mother_ext father $father_paired
	echo "Father mapping successful.";
	./scripts/to_get_vcf_files.sh references/reference.fasta daughter_1.$mother_ext daughter_2.$mother_ext daughter $daughter_paired
	echo "Daughter mapping successful.";
	./scripts/to_get_vcf_files.sh references/reference.fasta son_1.$mother_ext son_2.$mother_ext son $son_paired
	echo "Son mapping successful.";

	wait;

	#NOW run Trinity to assemble male contigs
	#in: male reads out: reference_male.fasta
#<<PREVENT_TRINITY_MALES
	if [[ $father_paired =~ (paired) ]] && [[ $son_paired =~ (paired) ]]; then
	    $trinity --CPU $PBS_NUM_PPN_used --seqType $male_ext --JM 20G --left input/father_and_sons_1.$male_ext --right input/father_and_sons_2.$male_ext --output trinity_out_dir_male 1>$trinity_stdout 2>&1
	    echo "$trinity --CPU $PBS_NUM_PPN_used --seqType $male_ext --JM 20G --left input/father_and_sons_1.$male_ext --right input/father_and_sons_2.$male_ext --output trinity_out_dir_male 1>$trinity_stdout 2>&1";
	else
	    $trinity --CPU $PBS_NUM_PPN_used --seqType $male_ext --JM 20G --single input/father_and_sons_1.$male_ext --output trinity_out_dir_male 1>$trinity_stdout 2>&1
	    echo "$trinity --CPU $PBS_NUM_PPN_used --seqType $male_ext --JM 20G --single input/father_and_sons_1.$male_ext --output trinity_out_dir_male 1>$trinity_stdout 2>&1";
	fi

	#retrieve assembled contigs and name them as reference_male.fasta
	mv trinity_out_dir_male/Trinity.fasta reference_male_pro.fasta
	perl -pe 's/(>[\S]+).+/$1/' reference_male_pro.fasta >references/reference_male.fasta; rm reference_male_pro.fasta;
#PREVENT_TRINITY_MALES

	grep ">" references/reference_male.fasta | sed 's/>//g' >references/male_contig_names

	#now call to_get_vcf_files.sh to map reads to reference contigs
	./scripts/to_get_Y_variants.sh references/reference_male.fasta mother_1.$mother_ext mother_2.$mother_ext mother $mother_paired
	echo "Mother mapping to males successful.";
	./scripts/to_get_Y_variants.sh references/reference_male.fasta father_1.$mother_ext father_2.$mother_ext father $father_paired
	echo "Father mapping to males successful.";
	./scripts/to_get_Y_variants.sh references/reference_male.fasta daughter_1.$mother_ext daughter_2.$mother_ext daughter $daughter_paired
	echo "Daughter mapping to males successful.";
	./scripts/to_get_Y_variants.sh references/reference_male.fasta son_1.$mother_ext son_2.$mother_ext son $son_paired
	echo "Son mapping to males successful.";

	#index bam files
	
	index_bam_file () 
	{
	  for ARG in "$@";
	    do
		if [ -e "bam/aln_cleaned_sorted_deduplicated_${ARG}.bam.bai" ];
		then	
			echo "Index already exists. Not being created again.";
		else
			samtools index bam/aln_cleaned_sorted_deduplicated_${ARG}.bam &
		fi
	    done;
	}

	#index bam files
	index_bam_file  mother father daughter son mother_male father_male daughter_male son_male;
	wait;
	echo "Indexes successfully created."
	
	echo -e "Starting analysis";

	#A variant X1X1 X2Y
	dir="A/";
	bash -x ./A.sh $email_address_of_user;
	perl scripts/sorting.pl A/;

	#Y variant
	dir="Y/";
	bash -x ./Y.sh $email_address_of_user;
	
	wait;
	
	#sending results (not BAM files)
	mutt -s "LINKYX: Results of computation for Y-linked genes" $email_address_of_user -a Y_results_sequences.txt < messages_to_user/message_results_sentY;
	mutt -s "LINKYX: Results of computation for X-linked genes" $email_address_of_user -a X_results_sequences.txt < messages_to_user/message_results_sentX;


echo -e "Done."
else 
	echo "not all input files are present in proper form";
	mutt -s "LINKYX: Not all input files are present in proper form." $email_address_of_user < messages_to_user/message_input_files_error
fi