Mercurial > repos > dawe > srf2fastq
view srf2fastq/io_lib-1.12.2/tests/srf_index.test @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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#!/bin/sh # Extract an entry using srf_extract_linear chmod u+w $outdir/proc.srf $top_builddir/progs/srf_extract_linear $outdir/proc.srf test_run:4:134:369:182 > $outdir/_.srf cmp $outdir/_.srf $srcdir/data/test_run_4_134_369_182.srf || exit 1 # Extract using the hash table method - should fail echo "NB: The next line is expected to be an error message" 1>&2 $top_builddir/progs/srf_extract_hash $outdir/proc.srf test_run:4:134:369:182 > $outdir/_.srf [ $? = 1 ] || exit 1 # Index it $top_builddir/progs/srf_index_hash $outdir/proc.srf cmp $outdir/proc.srf $srcdir/data/proc.srf.indexed || exit 1 # Extract using the hash table method $top_builddir/progs/srf_extract_hash $outdir/proc.srf test_run:4:134:369:182 > $outdir/_.srf [ $? = 0 ] || exit 1 # Check the archive/name access method too seq=`$top_builddir/progs/extract_seq $outdir/proc.srf/test_run:4:134:369:182 | tr -d '\012\015'` [ "$seq" = "GGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGTCTGGAAACGTACGGATTGTTCAGTAACTTGACTCAT" ] || exit 1