Mercurial > repos > bcclaywell > microbiome_pplacer_suite

diff filter-wrapper.sh @ 0:d4690e65afcd draft
Uploaded
author: bcclaywell
date: Thu, 26 Feb 2015 18:16:36 -0500
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter-wrapper.sh	Thu Feb 26 18:16:36 2015 -0500
@@ -0,0 +1,48 @@
+#!/bin/bash
+
+source $(dirname $0)/util.sh
+source $1
+
+INPUT_QUAL=$(extify qual ${INPUT_QUAL})
+BARCODES=$(extify csv ${BARCODES})
+RAW_SEQS=$(extify fasta ${RAW_SEQS})
+
+seqmagick quality-filter \
+    --input-qual ${INPUT_QUAL} \
+    --barcode-file ${BARCODES} \
+    --primer "${PRIMER}" \
+    --report-out ${FILTER_REPORT} \
+    --details-out ${FILTER_DETAILS} \
+    --map-out ${SPLIT_MAP} \
+    --barcode-header \
+    --min-length ${MIN_LENGTH} \
+    --min-mean-quality ${MIN_QUALITY} \
+    --quality-window 30 \
+    --quality-window-prop 0.9 \
+    --quality-window-mean-qual 15 \
+    ${RAW_SEQS} \
+    filtered.fasta
+
+if [[ ${REVERSE_COMPLEMENT} == "TRUE" ]]; then
+    seqmagick mogrify \
+        --reverse-complement \
+        filtered.fasta
+fi
+
+mv filtered.fasta ${FILTERED_SEQS}
+
+# TODO: separate tool for concatenating seq data (and reverse complementing them?)
+#cat [12]*Reads.fasta | seqmagick convert --input-format fasta - combined.fasta --reverse-complement
+#cat [12]*.map.csv > combined.map.csv
+
+sequencing_quality_report.py ${PLATE_JSON} -t "Sequencing quality report" -o ${SQR_DIR}
+
+cat <<EOF > ${SQR}
+<!DOCTYPE HTML>
+<html lang="en-US">
+  <head/>
+  <body>
+    <a href="index.html">Sequencing quality report</a>
+  </body>
+</html>
+EOF