From 96bcf78802267e8bb1834c06ffb98c5d700273e3 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 31 Aug 2020 20:41:19 -0500
Subject: [PATCH] se/pe fix
---
alignment/rnaseqalign.sh | 46 ++++++++++++++++++++++---------------
preproc_fastq/trimgalore.sh | 41 ++++++++++++++++++---------------
2 files changed, 49 insertions(+), 38 deletions(-)
diff --git a/alignment/rnaseqalign.sh b/alignment/rnaseqalign.sh
index 1e590c9..451a6c6 100755
--- a/alignment/rnaseqalign.sh
+++ b/alignment/rnaseqalign.sh
@@ -45,35 +45,43 @@ if [[ -z $NPROC ]]
then
NPROC=`nproc`
fi
-
-fqs=''
-i=0
-numfq=${#fqs[@]}
-while [[ $i -le $numfq ]]
-do
- fqs="$fqs $1"
- i=$((i + 1))
- shift 1
-done
-hisat_opt=''
-diff $fq1 $fq2 > difffile
if [[ -f $fq1 ]]
then
fqs="$fq1"
+ if [[ -f $fq2 ]]
+ then
+ diff $fq1 $fq2 > difffile
+ if [[ -s difffile ]]
+ then
+ fqs+=" $fq2"
+ fi
+ fi
+else
+ fqs=''
+ i=0
+ numfq=${#fqs[@]}
+ while [[ $i -le $numfq ]]
+ do
+ fqs="$fqs $1"
+ i=$((i + 1))
+ shift 1
+ done
fi
-if [[ -f $fq2 ]] && [[ -s difffile ]]
-then
- fqs+=" $fq2"
-fi
-numfq=${#fqs[@]}
+numfq=0
+for k in $fqs
+do
+ numfq=$((numfq + 1))
+done
+hisat_opt=''
star_opt=$fqs
fqarray=($fqs)
-if [[ $numfq == 1 ]]
+
+if [[ $numfq == 2 ]]
then
hisat_opt="-1 ${fqarray[0]} -2 ${fqarray[1]}"
else
- hisat_opt="-U $fqarray[0]"
+ hisat_opt="-U ${fqarray[0]}"
fi
if [ $algo == 'star' ]
diff --git a/preproc_fastq/trimgalore.sh b/preproc_fastq/trimgalore.sh
index aadd30e..859cd16 100644
--- a/preproc_fastq/trimgalore.sh
+++ b/preproc_fastq/trimgalore.sh
@@ -29,29 +29,32 @@ if [[ -z $pair_id ]]; then
usage
fi
fqs=''
-i=0
-numfq=${#fqs[@]}
-while [[ $i -le $numfq ]]
-do
- fqs="$fqs $1"
- i=$((i + 1))
- shift 1
-done
-
-if [[ -f $fq1 ]]
+if [[ -z $fq1 ]]
then
+ i=0
+ numfq=${#fqs[@]}
+ while [[ $i -le $numfq ]]
+ do
+ fqs="$fqs $1"
+ i=$((i + 1))
+ shift 1
+ done
+else
fqs="$fq1"
r1base="${fq1%.fastq*}"
+ if [[ -f $fq2 ]]
+ then
+ fqs+=" $fq2"
+ r2base="${fq2%.fastq*}"
+ fi
fi
-if [[ -f $fq2 ]]
-then
- fqs+=" $fq2"
- r2base="${fq2%.fastq*}"
-fi
-
-numfq=${#fqs[@]}
+numfq=0
+for k in $fqs
+do
+ numfq=$((numfq + 1))
+done
copts='-q 25 --illumina --gzip --length 35'
-if [[ $numfq == 1 ]]
+if [[ $numfq == 2 ]]
then
copts="$copts --paired"
fi
@@ -70,7 +73,7 @@ then
mv *_val_2.fq.gz ${pair_id}.trim.R2.fastq.gz
else
mv *_trimmed.fq.gz ${pair_id}.trim.R1.fastq.gz
- cp ${pair_id}.trim.R1.fastq.gz ${pair_id}.trim.R2.fastq.gz
+ #cp ${pair_id}.trim.R1.fastq.gz ${pair_id}.trim.R2.fastq.gz
fi
if [[ $filter == 1 ]]
--
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