partis-bcr 1.0.12.post1.dev3__cp312-cp312-macosx_10_13_universal2.whl → 1.0.12.post1.dev4__cp312-cp312-macosx_10_13_universal2.whl

test/paired/new-results/partition-new-simu-annotation-performance/plots/true-pair-clean-performance.svg

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test/paired/new-results/run-times.csv

@@ -1,7 +1,7 @@
 name,seconds
-cache-parameters-simu,19.8
-partition-new-simu,32.0
-subset-partition-new-simu,114.9
-seed-partition-new-simu,17.8
-get-selection-metrics-new-simu,10.9
-cache-parameters-data,34.3
+cache-parameters-simu,34.7
+partition-new-simu,42.0
+subset-partition-new-simu,155.0
+seed-partition-new-simu,22.6
+get-selection-metrics-new-simu,16.1
+cache-parameters-data,44.8

test/paired/new-results/subset-partition-new-simu/isub-0/partition.log

@@ -39,34 +39,34 @@ caching parameters
   vsearch: 24 / 24 v annotations (0 failed) with 8 v genes in 0.1 sec
     keeping 6 / 198 v genes
 smith-waterman  (new-allele fitting)
-  vsearch: 24 / 24 v annotations (0 failed) with 6 v genes in 0.0 sec
+  vsearch: 24 / 24 v annotations (0 failed) with 6 v genes in 0.1 sec
     running 10 procs for 24 seqs
       info for 24 / 24 = 1.000   (removed: 0 failed)
       kept 11 (0.458) unproductive
-    water time: 0.2  (ig-sw 0.0  processing 0.2)
+    water time: 0.2  (ig-sw 0.0  processing 0.1)
 smith-waterman  (writing parameters)
   vsearch: 24 / 24 v annotations (0 failed) with 6 v genes in 0.1 sec
     running 10 procs for 24 seqs
       info for 24 / 24 = 1.000   (removed: 0 failed)
       kept 11 (0.458) unproductive
         writing sw results to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml
-    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw (0.8 sec)
-    water time: 1.1  (ig-sw 0.9  processing 0.2)
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw (1.0 sec)
+    water time: 1.3  (ig-sw 1.2  processing 0.2)
   writing hmms     removed 21 genes from glfo (leaving v 6  d 13  j 4)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.6 sec)
+(0.9 sec)
 hmm
     reading output
         read 24 hmm output lines with 24 sequences in 24 events  (0 failures)
-    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm (0.7 sec)
-         infra time: 0.8
-      hmm step time: 1.3
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm (1.0 sec)
+         infra time: 1.1
+      hmm step time: 1.9
   writing hmms     removed 4  genes from glfo (leaving v 6  d 9  j 4)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.6 sec)
-      total time: 4.2
+(0.8 sec)
+      total time: 5.6
 cache-parameters igk:
 run partis cache-parameters --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igk.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
   --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -74,12 +74,12 @@ caching parameters
   vsearch: 18 / 18 v annotations (0 failed) with 6 v genes in 0.1 sec
     keeping 5 / 64 v genes
 smith-waterman  (new-allele fitting)
-  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
+  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
     running 10 procs for 18 seqs
     running 11 procs for 2 seqs
       info for 18 / 18 = 1.000   (removed: 0 failed)
       kept 5 (0.278) unproductive
-    water time: 0.3  (ig-sw 0.0  processing 0.2)
+    water time: 0.3  (ig-sw 0.0  processing 0.1)
 smith-waterman  (writing parameters)
   vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
     running 10 procs for 18 seqs
@@ -87,23 +87,23 @@ smith-waterman  (writing parameters)
       info for 18 / 18 = 1.000   (removed: 0 failed)
       kept 5 (0.278) unproductive
         writing sw results to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
-    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw (0.6 sec)
-    water time: 1.0  (ig-sw 0.7  processing 0.2)
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw (1.4 sec)
+    water time: 1.9  (ig-sw 1.5  processing 0.2)
   writing hmms     removed 2  genes from glfo (leaving v 5  d 1  j 5)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.4 sec)
+(0.9 sec)
 hmm
     reading output
         read 18 hmm output lines with 18 sequences in 18 events  (0 failures)
-    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm (0.6 sec)
-         infra time: 0.7
-      hmm step time: 1.0
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm (0.8 sec)
+         infra time: 1.2
+      hmm step time: 1.8
   writing hmms     removed 0  genes from glfo (leaving v 5  d 1  j 5)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.4 sec)
-      total time: 3.7
+(0.7 sec)
+      total time: 6.1
 cache-parameters igl:
 run partis cache-parameters --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igl.fa --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml
   --input-metafnames: added meta info for 10 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -111,19 +111,19 @@ caching parameters
   vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.1 sec
     keeping 3 / 80 v genes
 smith-waterman  (new-allele fitting)
-  vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.2 sec
+  vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.1 sec
     running 10 procs for 10 seqs
       info for 10 / 10 = 1.000   (removed: 0 failed)
       kept 7 (0.700) unproductive
-    water time: 0.2  (ig-sw 0.0  processing 0.1)
+    water time: 0.2  (ig-sw 0.0  processing 0.2)
 smith-waterman  (writing parameters)
-  vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.1 sec
+  vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.2 sec
     running 10 procs for 10 seqs
       info for 10 / 10 = 1.000   (removed: 0 failed)
       kept 7 (0.700) unproductive
         writing sw results to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml
-    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw (0.4 sec)
-    water time: 0.6  (ig-sw 0.5  processing 0.2)
+    writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw (0.5 sec)
+    water time: 0.8  (ig-sw 0.6  processing 0.2)
   writing hmms     removed 7  genes from glfo (leaving v 3  d 1  j 2)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
@@ -132,13 +132,13 @@ hmm
     reading output
         read 10 hmm output lines with 10 sequences in 10 events  (0 failures)
     writing parameters to test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/hmm (0.4 sec)
-         infra time: 0.4
-      hmm step time: 0.7
+         infra time: 0.6
+      hmm step time: 1.0
   writing hmms     removed 0  genes from glfo (leaving v 3  d 1  j 2)
 
   note: utils.memory_usage_fraction() needs testing on platform 'Darwin' to make sure unit conversions don't need changing
-(0.2 sec)
-      total time: 2.4
+(0.3 sec)
+      total time: 3.1
 partition igh:
 run partis partition --locus igh --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/single-chain/partition-igh.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml
   --input-metafnames: added meta info for 24 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
@@ -150,66 +150,66 @@ smith-waterman
       kept 11 (0.458) unproductive
         water time: 0.0
 hmm
-  caching all 24 naive sequences (0.5s)
+  caching all 24 naive sequences (0.8s)
     collapsed 24 queries into 22 clusters with identical naive seqs (0.0 sec)
-  22 clusters with 10 procs (0.4s)
-   22 clusters with 7 procs (0.4s)
-   20 clusters with 5 procs (0.4s)
-   18 clusters with 3 procs (0.4s)
+  22 clusters with 10 procs (0.5s)
+   22 clusters with 7 procs (0.8s)
+   20 clusters with 5 procs (0.5s)
+   18 clusters with 3 procs (0.5s)
    14 clusters with 2 procs (0.4s)
-   12 clusters with 1 proc (0.3s)
+   12 clusters with 1 proc (0.4s)
    note not merging entire cpath history
-      partition loop time: 2.3
+      partition loop time: 3.3
 getting annotations for final partition
-  subcluster annotating 12 clusters with steps:  (0.5s) (0.2s) 
-    subcluster annotation time 0.7
-      total time: 3.6
+  subcluster annotating 12 clusters with steps:  (0.6s) (0.3s) 
+    subcluster annotation time 0.9
+      total time: 5.1
 partition igk:
 run partis partition --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/single-chain/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
   --input-metafnames: added meta info for 18 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
 partitioning     (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm)
 smith-waterman
-  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.0 sec
+  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
       info for 18 / 18 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 5 (0.278) unproductive
         water time: 0.0
 hmm
-  caching all 18 naive sequences (0.3s)
+  caching all 18 naive sequences (0.5s)
     collapsed 18 queries into 7 clusters with identical naive seqs (0.0 sec)
   reducing n procs to number of clusters: 10 --> 7
   7 clusters with 7 procs (0.3s)
-   7 clusters with 5 procs (0.2s)
+   7 clusters with 5 procs (0.3s)
    7 clusters with 3 procs (0.2s)
-   7 clusters with 2 procs (0.2s)
-   7 clusters with 1 proc (0.3s)
-       partition loop time: 1.2
+   7 clusters with 2 procs (0.3s)
+   7 clusters with 1 proc (0.4s)
+       partition loop time: 1.4
 getting annotations for final partition
-  subcluster annotating 6 clusters with steps:  (0.3s) (0.2s) 
-    subcluster annotation time 0.5
-      total time: 2.2
+  subcluster annotating 6 clusters with steps:  (0.5s) (0.2s) 
+    subcluster annotation time 0.8
+      total time: 2.9
 partition igl:
 run partis partition --locus igl --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igl.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/single-chain/partition-igl.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml
   --input-metafnames: added meta info for 10 sequences from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml: loci paired-uids
 partitioning     (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/hmm)
 smith-waterman
-  vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.2 sec
+  vsearch: 10 / 10 v annotations (0 failed) with 3 v genes in 0.1 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igl/sw-cache.yaml
       info for 10 / 10 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 7 (0.700) unproductive
         water time: 0.0
 hmm
-  caching all 10 naive sequences (0.3s)
+  caching all 10 naive sequences (0.4s)
     collapsed 10 queries into 3 clusters with identical naive seqs (0.0 sec)
   reducing n procs to number of clusters: 10 --> 3
-  3 clusters with 3 procs (0.2s)
+  3 clusters with 3 procs (0.3s)
    3 clusters with 2 procs (0.2s)
-   3 clusters with 1 proc (0.2s)
-       partition loop time: 0.6
+   3 clusters with 1 proc (0.3s)
+       partition loop time: 0.7
 getting annotations for final partition
-  subcluster annotating 3 clusters with steps:  (0.2s) (0.2s) 
-    subcluster annotation time 0.3
-      total time: 1.4
+  subcluster annotating 3 clusters with steps:  (0.3s) (0.2s) 
+    subcluster annotation time 0.5
+      total time: 1.7
 combining chains
 cleaning pair info for 52 seqs
      synchronized/fixed 0 pairs where one had no pair info after cleaning: h 0  k 0  l 0
@@ -241,9 +241,9 @@ smith-waterman
       kept 6 (0.375) unproductive
         water time: 0.0
 hmm
-  subcluster annotating 8 clusters with steps:  (0.3s) (0.2s) 
-    subcluster annotation time 0.5
-      total time: 0.6
+  subcluster annotating 8 clusters with steps:  (0.4s) (0.2s) 
+    subcluster annotation time 0.6
+      total time: 0.7
   need to get annotations for 5/8 joint igk clusters
 annotate igh+igk: igk
 run partis annotate --locus igk --dont-write-git-info --max-ccf-fail-frac 0.15 --random-seed 1 --n-procs 10 --input-metafnames test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/meta-igk.yaml --infname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/input-seqs-igk.fa --outfname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igk.yaml --refuse-to-cache-parameters --parameter-dir test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk --sw-cachefname test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml --ignore-sw-pair-info --input-partition-fname test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igk-only-partition.yaml
@@ -251,15 +251,15 @@ hmm
   --input-partition-fname: read best partition with 18 sequences in 8 clusters from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igk/partition-igk-only-partition.yaml
 annotating    (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/hmm)
 smith-waterman
-  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.1 sec
+  vsearch: 18 / 18 v annotations (0 failed) with 5 v genes in 0.2 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igk/sw-cache.yaml
       info for 18 / 18 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 5 (0.278) unproductive
         water time: 0.0
 hmm
-  subcluster annotating 8 clusters with steps:  (0.3s) (0.2s) 
-    subcluster annotation time 0.5
-      total time: 0.7
+  subcluster annotating 8 clusters with steps:  (0.5s) (0.2s) 
+    subcluster annotation time 0.7
+      total time: 0.9
 igh+igl: synchronizing heavy and light chain cluster paths
     removing badly + unpaired seqs:  kept 0 total unpaired (i.e. setting aside in order to reintegrate after paired clustering): h 0  l 0
             note: discarding unpaired seqs in families with no (well-)paired seqs (i.e. families that are all either unpaired or paired to the other/wrong light chain), rather than keeping track of them to re-add later
@@ -282,14 +282,14 @@ hmm
   --input-partition-fname: read best partition with 7 sequences in 3 clusters from test/paired/new-results/subset-partition-new-simu/isub-0/igh+igl/partition-igh-only-partition.yaml
 annotating    (with test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/hmm)
 smith-waterman
-  vsearch: 7 / 7 v annotations (0 failed) with 2 v genes in 0.2 sec
+  vsearch: 7 / 7 v annotations (0 failed) with 2 v genes in 0.1 sec
         reading sw results from test/paired/new-results/subset-partition-new-simu/isub-0/parameters/igh/sw-cache.yaml
       info for 7 / 7 = 1.000   (removed: 0 failed, 0 duplicates [removed when cache file was written])
       kept 4 (0.571) unproductive
         water time: 0.0
 hmm
-  subcluster annotating 3 clusters with steps:  (0.2s) (0.2s) 
-    subcluster annotation time 0.4
+  subcluster annotating 3 clusters with steps:  (0.3s) (0.2s) 
+    subcluster annotation time 0.5
       total time: 0.6
   need to get annotations for 2/3 joint igl clusters
 annotate igh+igl: igl
@@ -305,7 +305,7 @@ smith-waterman
       kept 6 (0.857) unproductive
         water time: 0.0
 hmm
-  subcluster annotating 3 clusters with steps:  (0.2s) (0.2s) 
+  subcluster annotating 3 clusters with steps:  (0.2s) (0.1s) 
     subcluster annotation time 0.4
       total time: 0.5
   --input-metafnames: no meta info added from test/paired/new-results/subset-partition-new-simu/isub-0/meta.yaml
@@ -320,4 +320,4 @@ hmm
         h   12 --> 11   -1
         k    6 --> 8    +2
         l    3 --> 3   
-      total time: 39.9
+      total time: 53.7