From: Tom Clegg <tom@tomclegg.ca>
Date: Wed, 2 Dec 2020 20:49:20 +0000 (-0500)
Subject: Update example.
X-Git-Url: https://git.arvados.org/lightning.git/commitdiff_plain/ce865ddd069ce116fec7acb529dd1df9b730024b

Update example.

Arvados-DCO-1.1-Signed-off-by: Tom Clegg <tom@tomclegg.ca>
---

diff --git a/example-su92l-1kg.sh b/example-su92l-1kg.sh
index abb696440d..c60e8fc93d 100755
--- a/example-su92l-1kg.sh
+++ b/example-su92l-1kg.sh
@@ -19,13 +19,20 @@ genome=$(lightning     ref2genome   -project ${project} -priority ${priority} -r
 fasta=$(lightning      vcf2fasta    -project ${project} -priority ${priority} -ref ${ref_fa} -genome ${genome} -mask=true ${gvcf})                     ; echo fasta=${fasta}
 # fasta=su92l-4zz18-9nq05jifgz7iult
 
-ref37_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -save-incomplete-tiles ${ref37_fa}) ; echo ref37_lib=${ref37_lib}
+ref37_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -save-incomplete-tiles=true ${ref37_fa}) ; echo ref37_lib=${ref37_lib}
 # ref37_lib=su92l-4zz18-vnhlv3g6yp1azls/library.gob
 # 539s
+# ref37_lib=su92l-4zz18-v0xfm2o1tu3u1w3/library.gob.gz
+# 2751s @ 4a3899f
 
-ref38_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -save-incomplete-tiles ${ref_fa}) ; echo ref38_lib=${ref38_lib}
+ref38_lib=$(lightning  import       -project ${project} -priority ${priority} -tag-library ${tagset} -skip-ooo=true -output-tiles=true -save-incomplete-tiles=true ${ref_fa}) ; echo ref38_lib=${ref38_lib}
 # ref38_lib=su92l-4zz18-swebknshfwsvys6/library.gob
 
+bed37=$(lightning export       -project ${project} -priority ${priority} -i ${ref37_lib} -output-format hgvs -ref /mnt/$ref37_fa -output-bed hg37.bed) ; echo bed37=${bed37}
+# bed37=su92l-4zz18-gb3hihiiaz0xaz9/export.csv
+# 463s @ 870319f
+bed38=$(lightning export       -project ${project} -priority ${priority} -i ${ref38_lib} -output-format hgvs -ref /mnt/$ref_fa -output-bed hg38.bed) ; echo bed38=${bed38}
+
 unfiltered=$(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
@@ -53,21 +60,34 @@ filtered=$(lightning   filter       -project ${project} -priority ${priority} -i
 
 annotations=$(lightning annotate    -project ${project} -priority ${priority} -i ${merged})                                                            ; echo annotations=${annotations}
 
-pca=$(lightning        pca-go       -project ${project} -priority ${priority} -i ${filtered} -one-hot)                                                 ; echo pca=${pca}
+pca=$(lightning        pca-go       -project ${project} -priority ${priority} -i ${unfiltered} -min-coverage "0.9" -max-variants "30")                 ; echo pca=${pca}
+# pca=su92l-4zz18-e3xhi2mzp8rqevd/pca.npy
+# 3987s @ c237c16
 plot=$(lightning       plot         -project ${project} -priority ${priority} -i ${pca} -labels-csv ${info}/sample_info.csv -sample-fasta-dir ${fasta})
 echo >&2 "https://workbench2.${plot%%-*}.arvadosapi.com/collections/${plot}"
 echo ${plot%%/*}
-
+# plot=su92l-4zz18-xyei3lnyxmgo7lh/plot.png
+# 535s @ c237c16
 
 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
+# merged38=su92l-4zz18-nq8dmtng68ozovu/library.gob.gz
+# 9803s @ 69b71af
 
 numpy=$(lightning      export-numpy -project ${project} -priority ${priority} -i ${merged38})                                                          ; echo numpy=${numpy}
 # numpy=su92l-4zz18-w3dx5k79mtbz6qt/matrix.npy
 # 6155s
+# numpy=su92l-4zz18-g1y2eg9qvngvkkq/matrix.npy
+# 6633s @ 83983ad
+# numpy=su92l-4zz18-cpw0i3z7wery77o/matrix.npy
+# 6311s @ 4e6ada0
+# numpy=su92l-4zz18-hljgbqs6c87wles/matrix.npy
+# 6824s @ 2e1cb2e
+# numpy=su92l-4zz18-vw31l0qzenyb44l/matrix.npy
+# 7403s @ 6785271
 # pcapy=$(lightning      pca          -project ${project} -priority ${priority} -i ${numpy})                                                             ; echo pcapy=${pcapy}
 comvar=$(lightning     numpy-comvar -project ${project} -priority ${priority} -i ${numpy} -annotations ${numpy%/matrix.npy}/annotations.tsv)           ; echo comvar=${comvar}
 # comvar=su92l-4zz18-s1yhngobdvcoc2e/commonvariants.csv