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#!/bin/bash
CUR_DIR=`pwd`
if [ "$AUTOPKGTEST_TMP" = "" ]; then
AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXX`
trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
fi
mkdir -p "$AUTOPKGTEST_TMP"/tests
# Copy configuration file
cp -a "${CUR_DIR}"/utils/nominal.ini "$AUTOPKGTEST_TMP"/tests
cd "$AUTOPKGTEST_TMP"/tests/
# Download Data
wget http://gembox.cbcb.umd.edu/mhap/raw/ecoli_p4_filtered.fastq.gz
# Extract Data
gunzip ecoli_p4_filtered.fastq.gz
seqtk seq -a ecoli_p4_filtered.fastq > reads.fasta
hinge correct-head reads.fasta reads.pb.fasta map.txt
fasta2DB ecoli reads.fasta
DBsplit -x500 -s100 ecoli
HPC.daligner -t5 ecoli | bash -v
LAmerge ecoli.las ecoli.[1-5].las
rm ecoli.*.las
DAScover -v -H10000 -mrepeat_mask ecoli.db ecoli.las
DASqv -c100 ecoli ecoli.las
# Run filter
mkdir log
hinge filter --db ecoli --las ecoli.las -x ecoli --config nominal.ini
# Get maximal reads
hinge maximal --db ecoli --las ecoli.las -x ecoli --config nominal.ini
# Run layout
hinge layout --db ecoli --las ecoli.las -x ecoli --config nominal.ini -o ecoli
# Run postprocessing ( networkx version needs to be downgraded to 1.x )
hinge clip ecoli.edges.hinges ecoli.hinge.list demo
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