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Export labels.csv with numpy array.
[lightning.git]
/
example-su92l-1kg.sh
diff --git
a/example-su92l-1kg.sh
b/example-su92l-1kg.sh
index c4e2b543869fa9fa259090ab2995b98f69e72c83..abb696440d8065e020834c4f317f247683a9735b 100755
(executable)
--- a/
example-su92l-1kg.sh
+++ b/
example-su92l-1kg.sh
@@
-28,6
+28,12
@@
ref38_lib=$(lightning import -project ${project} -priority ${priority} -t
unfiltered=$(lightning import -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true ${fasta}) ; echo unfiltered=${unfiltered}
# unfiltered=su92l-4zz18-mz3546bib6oj1gg/library.gob
unfiltered=$(lightning import -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true ${fasta}) ; echo unfiltered=${unfiltered}
# unfiltered=su92l-4zz18-mz3546bib6oj1gg/library.gob
+# unfiltered=su92l-4zz18-72ovi5qrderxudv/library.gob
+# 24674s @ pre-38e6e7c
+# unfiltered=su92l-4zz18-ywhkc1hgdzxwp5u/library.gob
+# 18497s @ 64vcpu bf0968a
+# _____s @ 32vcpu 83983ad
+
merged=$(lightning merge -project ${project} -priority ${priority} ${unfiltered} ${ref37_lib}) ; echo merged=${merged}
# merged=su92l-4zz18-svw5xqe5g0ct2v1/library.gob
merged=$(lightning merge -project ${project} -priority ${priority} ${unfiltered} ${ref37_lib}) ; echo merged=${merged}
# merged=su92l-4zz18-svw5xqe5g0ct2v1/library.gob
@@
-56,8
+62,10
@@
echo ${plot%%/*}
merged38=$(lightning merge -project ${project} -priority ${priority} ${unfiltered} ${ref38_lib}) ; echo merged38=${merged38}
# merged38=su92l-4zz18-xq17gtaltjxbm3n/library.gob
# 1602s
merged38=$(lightning merge -project ${project} -priority ${priority} ${unfiltered} ${ref38_lib}) ; echo merged38=${merged38}
# merged38=su92l-4zz18-xq17gtaltjxbm3n/library.gob
# 1602s
+# merged38=su92l-4zz18-5kcaci3hqzukjv2/library.gob
+# 2815s @ 83983ad
-numpy=$(lightning export-numpy -project ${project} -priority ${priority} -i ${merged38}
-max-variants "30" -min-coverage "0.9")
; echo numpy=${numpy}
+numpy=$(lightning export-numpy -project ${project} -priority ${priority} -i ${merged38}
)
; echo numpy=${numpy}
# numpy=su92l-4zz18-w3dx5k79mtbz6qt/matrix.npy
# 6155s
# pcapy=$(lightning pca -project ${project} -priority ${priority} -i ${numpy}) ; echo pcapy=${pcapy}
# numpy=su92l-4zz18-w3dx5k79mtbz6qt/matrix.npy
# 6155s
# pcapy=$(lightning pca -project ${project} -priority ${priority} -i ${numpy}) ; echo pcapy=${pcapy}