obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-12-10 01:30:27 +00:00
Code Issues Packages Projects Releases Wiki Activity

Accelerate the speed of very long fasta sequences, and more generaly of every format

Browse Source
This commit is contained in:
Eric Coissac
2025-03-12 13:29:41 +01:00
parent 83926c91e1
commit 3a1cf4fe97
8 changed files with 185 additions and 54 deletions
Download Patch File Download Diff File Expand all files Collapse all files

BIN
obitests/obitools/obiconvert/gbpln1088.4Mb.fasta.gz Normal file
View File

Binary file not shown.

35
obitests/obitools/obiconvert/test.sh
View File

@@ -13,6 +13,11 @@ CMD=obiconvert
#
######
TEST_DIR="$(dirname "$(readlink -f "${BASH_SOURCE[0]}")")"
if [ -z "$TEST_DIR" ] ; then
TEST_DIR="."
fi
OBITOOLS_DIR="${TEST_DIR/obitest*/}build"
export PATH="${OBITOOLS_DIR}:${PATH}"
@@ -99,6 +104,36 @@ else
fi
((ntest++))
if obiconvert -Z "${TEST_DIR}/gbpln1088.4Mb.fasta.gz" \
> "${TMPDIR}/xxx.fasta.gz" && \
zdiff "${TEST_DIR}/gbpln1088.4Mb.fasta.gz" \
"${TMPDIR}/xxx.fasta.gz"
then
log "$MCMD: converting large fasta file to fasta OK"
((success++))
else
log "$MCMD: converting large fasta file to fasta failed"
((failed++))
fi
((ntest++))
if obiconvert -Z --fastq-output \
"${TEST_DIR}/gbpln1088.4Mb.fasta.gz" \
> "${TMPDIR}/xxx.fastq.gz" && \
obiconvert -Z --fasta-output \
"${TMPDIR}/xxx.fastq.gz" \
> "${TMPDIR}/yyy.fasta.gz" && \
zdiff "${TEST_DIR}/gbpln1088.4Mb.fasta.gz" \
"${TMPDIR}/yyy.fasta.gz"
then
log "$MCMD: converting large file between fasta and fastq OK"
((success++))
else
log "$MCMD: converting large file between fasta and fastq failed"
((failed++))
fi
#########################################
#
# At the end of the tests