Mercurial > repos > dawe > srf2fastq
comparison 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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-1:000000000000 | 0:d901c9f41a6a |
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1 #!/bin/sh | |
2 # Extract an entry using srf_extract_linear | |
3 chmod u+w $outdir/proc.srf | |
4 $top_builddir/progs/srf_extract_linear $outdir/proc.srf test_run:4:134:369:182 > $outdir/_.srf | |
5 cmp $outdir/_.srf $srcdir/data/test_run_4_134_369_182.srf || exit 1 | |
6 | |
7 # Extract using the hash table method - should fail | |
8 echo "NB: The next line is expected to be an error message" 1>&2 | |
9 $top_builddir/progs/srf_extract_hash $outdir/proc.srf test_run:4:134:369:182 > $outdir/_.srf | |
10 [ $? = 1 ] || exit 1 | |
11 | |
12 # Index it | |
13 $top_builddir/progs/srf_index_hash $outdir/proc.srf | |
14 cmp $outdir/proc.srf $srcdir/data/proc.srf.indexed || exit 1 | |
15 | |
16 # Extract using the hash table method | |
17 $top_builddir/progs/srf_extract_hash $outdir/proc.srf test_run:4:134:369:182 > $outdir/_.srf | |
18 [ $? = 0 ] || exit 1 | |
19 | |
20 # Check the archive/name access method too | |
21 seq=`$top_builddir/progs/extract_seq $outdir/proc.srf/test_run:4:134:369:182 | tr -d '\012\015'` | |
22 [ "$seq" = "GGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGTCTGGAAACGTACGGATTGTTCAGTAACTTGACTCAT" ] || exit 1 | |
23 |