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#!/bin/bash
#
# add_samples_from_previous_runs.sh <config.sh> <project_id> <version> <samples>
#
#
CONFIG_SH=$1
PROJECT_ID=$2
VERSION=$3
SAMPLES=$4
source $CONFIG_SH
cd $PARAMS_DIR
# create reads directory for project and symlink directory underneath
mkdir -p $READS_DIR/$PROJECT_ID/symlinks
SHORT_PROJECT_ID=`echo $PROJECT_ID | cut -f 1 -d '_'`
N=`wc -l $SAMPLES | awk '{ print $1 }'`
for ((i = 1; i <= $N; i = i + 1))
do
FAMILY_ID=`head -n $i $SAMPLES | tail -n 1 | cut -f 1`
SAMPLE=`head -n $i $SAMPLES | tail -n 1 | cut -f 2`
SEX=`head -n $i $SAMPLES | tail -n 1 | cut -f 3`
PHENOTYPE=`head -n $i $SAMPLES | tail -n 1 | cut -f 4`
ORIGINAL_PROJECT_ID=`head -n $i $SAMPLES | tail -n 1 | cut -f 5`
ORIGINAL_SAMPLE_ID=`head -n $i $SAMPLES | tail -n 1 | cut -f 6`
PREFIX=${SHORT_PROJECT_ID}_${VERSION}_${FAMILY_ID}
# create symlinks for problematic filenames
mkdir -p $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE
for FILE in `ls $DOWNLOAD_DIR/$ORIGINAL_PROJECT_ID/*/*/*$ORIGINAL_SAMPLE_ID*/*_1_*_1.fastq.gz`
do
newname=`basename $FILE | sed -e 's/_1_/_one_/'`
ln -s $FILE $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/${newname%1.fastq.gz}R1.fastq.gz
done
for FILE in `ls $DOWNLOAD_DIR/$ORIGINAL_PROJECT_ID/*/*/*$ORIGINAL_SAMPLE_ID*/*_1_*_2.fastq.gz`
do
newname=`basename $FILE | sed -e 's/_1_/_one_/'`
ln -s $FILE $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/${newname%2.fastq.gz}R2.fastq.gz
done
for FILE in `ls $DOWNLOAD_DIR/$ORIGINAL_PROJECT_ID/*/*/*$ORIGINAL_SAMPLE_ID*/*_2_*_1.fastq.gz`
do
newname=`basename $FILE | sed -e 's/_2_/_two_/'`
ln -s $FILE $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/${newname%1.fastq.gz}R1.fastq.gz
done
for FILE in `ls $DOWNLOAD_DIR/$ORIGINAL_PROJECT_ID/*/*/*$ORIGINAL_SAMPLE_ID*/*_2_*_2.fastq.gz`
do
newname=`basename $FILE | sed -e 's/_2_/_two_/'`
ln -s $FILE $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/${newname%2.fastq.gz}R2.fastq.gz
done
# for FILE in `ls $READS_DIR/$PROJECT_ID/symlinks/$SAMPLE/*_R[1,2].fastq.gz`
# do
# echo "$FILE,$SAMPLE,$FAMILY_ID,$SEX,$PHENOTYPE,$TARGET" >> ${PREFIX}.csv
# done
done