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kstatebioinfo Updated test script to include unique steps
over 8 years ago
Commit id: 260847f23fac2577a1d860bb10af98bc1536460a
deletions | additions
diff --git a/figures/time_runs.sh b/figures/time_runs.sh
index a4a80ff..4c7b6fc 100644
--- a/figures/time_runs.sh
+++ b/figures/time_runs.sh
...
echo "Header whitespace only Fasta-O-Matic execution:"
/usr/bin/time -v python ~/read-cleaning-format-conversion/KSU_bioinfo_lab/fasta-o-matic/fasta_o_matic.py -f ~/test_fasta_o_matic/input/GCF_000164845.1_Vicugna_pacos-2.0.1_genomic_FAKE.fna -o ~/test_fasta_o_matic/out -c -s header_whitespace -q
echo "Unique only Fasta-O-Matic execution:"
/usr/bin/time -v python ~/read-cleaning-format-conversion/KSU_bioinfo_lab/fasta-o-matic/fasta_o_matic.py -f ~/test_fasta_o_matic/input/GCF_000164845.1_Vicugna_pacos-2.0.1_genomic_FAKE.fna -o ~/test_fasta_o_matic/out -c -s unique -q
echo "All steps Fasta-O-Matic execution:"
/usr/bin/time -v python ~/read-cleaning-format-conversion/KSU_bioinfo_lab/fasta-o-matic/fasta_o_matic.py -f ~/test_fasta_o_matic/input/GCF_000164845.1_Vicugna_pacos-2.0.1_genomic_FAKE.fna -o ~/test_fasta_o_matic/out1 -c
-s unique wrap new_line header_whitespace -q
echo "Wrap only setk execution:"
/usr/bin/time -v /home/bionano/seqtk/seqtk seq -l 60 /home/bionano/test_fasta_o_matic/input/GCF_000164845.1_Vicugna_pacos-2.0.1_genomic_FAKE.fna > /home/bionano/test_fasta_o_matic/out2/GCF_000164845.1_Vicugna_pacos-2.0.1_genomic_FAKE_seqtk_wrap.fna
echo "Wrap only seqret execution:"
/usr/bin/time -v /home/bionano/EMBOSS-6.5.7/emboss/seqret -sequence ~/test_fasta_o_matic/input/GCF_000164845.1_Vicugna_pacos-2.0.1_genomic_FAKE.fna -outseq /home/bionano/test_fasta_o_matic/out3/GCF_000164845.1_Vicugna_pacos-2.0.1_genomic_FAKE_seqret.fna