genomicsITER · August 9, 2017 17:11 · Sep 1, 2015 · Aug 29, 2015 · Aug 29, 2015 · Aug 29, 2015
diff --git a/subsample.sh b/subsample.sh
@@ -24,7 +24,7 @@ Optional:   'outdir' is the directory to put the subsampled files \n\
                 If not specified, we will use \n\
                 `pwd`
 \n\
-'seed' is the seed value to be used for all samples run during \n\
+            'seed' is the seed value to be used for all samples run during \n\
                 this instance. If not specified, a random number will \n\
                 be generated and recorded for posterity's sake \n\
 " >&2

diff --git a/subsample.sh b/subsample.sh
@@ -4,7 +4,7 @@ set -e
 set -u
 set -o pipefail
 
-#   A script to subsample
+#   A script to subsample Fasta/FastQ files using Seqtk
 if ! `command -v seqtk > /dev/null 2> /dev/null`
 then
     echo "Failed to find seqtk!"

diff --git a/subsample.sh b/subsample.sh
@@ -1,18 +1,84 @@
 #!/bin/bash
 
+set -e
+set -u
+set -o pipefail
+
+#   A script to subsample
 if ! `command -v seqtk > /dev/null 2> /dev/null`
 then
     echo "Failed to find seqtk!"
     exit 1
 fi
 
-SEED=`echo "$RANDOM"`
+#   Define a usage message
+function Usage() {
+    echo -e "\
+Usage:  subsample.sh sample_info frac [outdir] [seed]\n\
+\n\
+where:  'sample_info' is a Fasta/FastQ file to be subsampled \n\
+            or a list of Fasta/FastQ files to be subsampled \n\
+        'frac' is either the fraction or number of reads to be kept \n\
+\n\
+Optional:   'outdir' is the directory to put the subsampled files \n\
+                If not specified, we will use \n\
+                `pwd`
+\n\
+'seed' is the seed value to be used for all samples run during \n\
+                this instance. If not specified, a random number will \n\
+                be generated and recorded for posterity's sake \n\
+" >&2
+    exit 1
+}
+
+#   Do we have the two required arguments?
+if [ "$#" -lt 2 ]
+then
+    Usage
+fi
+
+#   Give the arguments names and set default values
+SAMPLE_INFO=$1
+FRAC=$2
+OUTDIR=${3:-`pwd`}
+SEED=${4:-`echo "$RANDOM"`}
 
+#   Make sure that the outdirectory exists
+mkdir -p ${OUTDIR}
+
+#   Define a function to carry out the subsampling
 function subsample() {
     sample="$1"
     seed="$2"
     frac="$3"
+    out="$4"
+    echo "Subsampling ${sample}"
     name=`basename "${sample}" | cut -d '.' -f 1`
     ext=`basename "${sample}" | cut -d '.' -f 2`
-    seqtk sample -s"${seed}" "${sample}" "${frac}" > "${name}"_sub_"${frac}"."${ext}"
+    seqtk sample -s"${seed}" "${sample}" "${frac}" > "${out}"/"${name}"_sub_"${frac}"."${ext}"
 }
+
+#   Export this function
+export -f subsample
+
+#   Get the first line of ${SAMPLE_INFO}
+LINE=`head -1 "${SAMPLE_INFO}"`
+
+#   See if this first line is a file
+if [[ -f "${LINE}" ]]
+then #  If so
+    if `command -v parallel > /dev/null 2> /dev/null` # See if we have GNU Parallel installed
+    then #  If so
+        cat "${SAMPLE_INFO}" | parallel "subsample {} ${SEED} ${FRAC} ${OUTDIR}" #  Run the subsample function on all files in parallel
+    else #  If we don't have parallel
+        for fastq in `cat "${SAMPLE_INFO}"` #   Run the subsample function in serial
+        do
+            subsample "$fastq" "${SEED}" "${FRAC}" "${OUTDIR}"
+        done
+    fi
+else #  If the first line doesn't point to a file, assume we were given a Fasta/FastQ file
+    subsample "${SAMPLE_INFO}" "${SEED}" "${FRAC}" "${OUTDIR}"
+fi
+
+#   Record what ${SEED} was, let us know where the final files can be found, and write all this to an out message file
+echo -e "`date`:\nWe used a seed value of ${SEED}\nAll subsampled files can be found at ${OUTDIR}\nThis message can be read again at ${OUTDIR}/outMSG.txt" | tee -a ${OUTDIR}/outMSG.txt
diff --git a/subsample.sh b/subsample.sh
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+if ! `command -v seqtk > /dev/null 2> /dev/null`
+then
+    echo "Failed to find seqtk!"
+    exit 1
+fi
+
+SEED=`echo "$RANDOM"`
+
+function subsample() {
+    sample="$1"
+    seed="$2"
+    frac="$3"
+    name=`basename "${sample}" | cut -d '.' -f 1`
+    ext=`basename "${sample}" | cut -d '.' -f 2`
+    seqtk sample -s"${seed}" "${sample}" "${frac}" > "${name}"_sub_"${frac}"."${ext}"
+}