pipe_fasta.sh

#!/usr/bin/env bash

# pipe_fasta.sh
#
#
# Created by Bruno Costa on 09/11/2015
# Copyright 2015 ITQB / UNL. All rights reserved.
# Copies fasta files to fasta folder to start work
# 
# Call: pipe_fasta.sh [Lib_first] [Lib_last] [template]
#

#Important if this script fails do not continue.
set -e

err_report() {
    >&2 echo "Error -  on line $1 caused a code $2 exit - $3"
    echo "Error -  on line $1 caused a code $2 exit - $3"
}
trap 'err_report $LINENO $? $(basename $0)' ERR






#Gets the script directory
DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )

#Get config settings
. $DIR/"config/workdirs.cfg"

#Setting up log dir
mkdir -p $workdir"/log/"
mkdir -p $workdir"/data/fasta"

SCRIPT_DIR=$DIR"/scripts/"
#Choses run mode based on input arguments
if [[ -z $2 || -z $3 ]]; then
  if [[ -z $2 ]]; then
    

    #Log uses input so has to go here.
    log_file=$workdir"/log/"$(date +"%y|%m|%d-%H:%M:%S")":PPID${PPID}:pipe_fasta.log"
    echo $(date +"%y/%m/%d-%H:%M:%S")" - "$(basename ${log_file}) 
    exec 2>&1 > ${log_file}


    #REVISE NOT FINISHED  ........ IS NOT IN USE
    #Only one argument was given
    convert_lib=$LCSCIENCE_LIB  #From config file?
    LIB=$LIB_FIRST   
    cp $convert_lib ${workdir}/data/fasta/Lib${LIB}.fa &
  else
    #Two arguments were given
    LIB_NOW=$1
    FILE=$2
    LIB=$(printf "%02d\n"  $LIB_NOW)  


    #Log uses input so has to go here.
    log_file=$workdir"/log/"$(date +"%y|%m|%d-%H:%M:%S")":PPID${PPID}:pipe_fasta-$(basename $FILE).log"
    echo $(date +"%y/%m/%d-%H:%M:%S")" - "$(basename ${log_file}) 
    exec 2>&1 > ${log_file}

    ##Needs dealing with gz files
    >&2 echo "Copying ${FILE}..." 
    cp $FILE ${workdir}/data/fasta/Lib${LIB}.fa  


  fi
else
  #Log uses input so has to go here.
  log_file=$workdir"/log/"$(date +"%y|%m|%d-%H:%M:%S")":PPID${PPID}:pipe_fasta:$1-$2.log"
  echo $(date +"%y/%m/%d-%H:%M:%S")" - "$(basename ${log_file}) 
  exec 2>&1 > ${log_file}

  LIB_FIRST=$1
  LIB_LAST=$2
  TEMPLATE=$3
  

  NPROC=0
  cycle=$(eval echo {${LIB_FIRST}..${LIB_LAST}})
  printf $(date +"%y/%m/%d-%H:%M:%S")" - Copying all fasta files to workdir\n"
  for i in $cycle
  do
    LIB_NOW=$i
    LIB=$(printf "%00d\n"  $LIB_NOW)  
    LIB_AFTER=$(printf "%02d\n"  $LIB_NOW)  
    #Issues here are if it searches for 1 it might get 11 likewise if it searched for 11 it might get 111 need te strikeout the possibility of a numeral.
    
    #Do fa fasta files exist?
    if [[ -z $(ls ${INSERTS_DIR} | grep -E ".*${TEMPLATE}0*${LIB}[^0-9].*(fa|fasta)+$") ]];then
        #Test if .fastq/fq.gz exists      
        if [[ ! -z $(ls ${INSERTS_DIR} | grep -E ".*${TEMPLATE}0*${LIB}[^0-9].*(fa|fasta)+\.gz$") ]];then
            extract_lib=$(ls ${INSERTS_DIR} | grep -E ".*${TEMPLATE}0*${LIB}[^0-9].*(fa|fasta)+\.gz$")
            archive="${INSERTS_DIR}/${extract_lib}"
            if [[ -f "${archive}" ]]; then
                NPROC=$(( $NPROC + 1 ))
                gunzip -c ${archive} > ${workdir}/data/fasta/Lib${LIB_AFTER}.fa &       
            else
                >&2 echo "Terminating. No files or multiple files found using: ${TEMPLATE}" 
                exit 1
            fi
        else
            >&2 echo "Terminating. No files using template: ${TEMPLATE},in: ${INSERTS_DIR}" 
            exit 1  
        fi
    else
        #Confirm fasta files exist
        if [[ -f ${INSERTS_DIR}/$(ls ${INSERTS_DIR} | grep -E ".*${TEMPLATE}0*${LIB}[^0-9].*(fa|fasta)+$") ]];then
            fasta=${INSERTS_DIR}/$(ls ${INSERTS_DIR} | grep -E ".*${TEMPLATE}0*${LIB}[^0-9].*(fa|fasta)+$")
            NPROC=$(($NPROC+1))
            #Change this to set for dynamic threading.
            cp ${fasta} ${workdir}/data/fasta/Lib${LIB_AFTER}.fa &
        else
            >&2 echo "Terminating. Multiple files found using template: ${TEMPLATE}, in: ${INSERTS_DIR}." 
            exit 1
        fi
    fi
    if [ "$NPROC" -ge "$THREADS" ]; then
        wait
        NPROC=0
    fi

  done
  wait  
fi

printf $(date +"%y/%m/%d-%H:%M:%S")" - Copied all fasta files\n"


ok_log=${log_file/.log/:OK.log}

mv $log_file $ok_log

duration=$(date -u -d @${SECONDS} +"%T")
printf "\n-----------END--------------\nThis script ran in ${duration}\n${SECONDS}sec.\nUsing ${THREADS} threads.\n"
echo $(basename $ok_log)

exit 0