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Merged
BarryDigby merged 1 commit into from
Sep 3, 2026
Merged

v1.0.2: multi-mappers to report, fix miRNA | RBP to use hg38 not circ… #10

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2 changes: 1 addition & 1 deletion assets/manuscript.svg
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7 changes: 5 additions & 2 deletions .../execution_report_2026-08-20_21-19-58.txt → .../execution_report_2026-09-03_12-55-30.txt
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@@ -1,7 +1,7 @@
pycircdb execution report
========================================
Timestamp : 2026-08-20 21:19:58
pycircdb version : 0.1.5
Timestamp : 2026-09-03 12:55:30
pycircdb version : 1.0.1
Database version : 1.0
Config file : /home/barry/Desktop/pycircdb/benchmarks/performance/configs/bench_100.json

Expand Down Expand Up @@ -58,13 +58,15 @@ Mapping Statistics
circpedia [84/100] 84.0%
cscd [95/100] 95.0%
exorbase [77/100] 77.0%

FASTA
arraystar [33/100] 33.0%
circRNADb [52/100] 52.0%
circbank [95/100] 95.0%
circbase [49/100] 49.0%
circpedia [84/100] 84.0%
cscd [95/100] 95.0%

miRNA
chr10 [7/100] 7.0%
chr11 [3/100] 3.0%
Expand All @@ -85,6 +87,7 @@ Mapping Statistics
chr7 [7/100] 7.0%
chr8 [4/100] 4.0%
chr9 [1/100] 1.0%

RBP
chr10 [7/100] 7.0%
chr11 [3/100] 3.0%
Expand Down
118 changes: 118 additions & 0 deletions benchmarks/performance/results/bench_1000/execution_report_2026-09-03_12-55-48.txt
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pycircdb execution report
========================================
Timestamp : 2026-09-03 12:55:48
pycircdb version : 1.0.1
Database version : 1.0
Config file : /home/barry/Desktop/pycircdb/benchmarks/performance/configs/bench_1000.json

Global Parameters
--------------------
max_tasks: 1
output_dir: benchmarks/performance/results/bench_1000
tmp_dir: tmp

Samples
--------------------
bench_1000:
file_path : benchmarks/performance/inputs/bench_1000.txt
reference : hg19

Databases & Algorithms
--------------------
Annotation databases : arraystar, circatlas, circbank, circbase, circpedia, circrnadb, cscd, exorbase
FASTA databases : arraystar, circbank, circbase, circpedia, circrnadb, cscd
miRNA algorithms : miRanda, PITA, TargetScan

Database Provenance
--------------------
Annotation
arraystar : hg19, version 2.0, accessed January 2025
circatlas : hg38, version 3.0, accessed January 2026
circbank : hg19, version 1.0, accessed January 2026
circbase : hg19, version 1.0, accessed January 2026
circpedia : hg38, version 3.0, accessed October 2025
circrnadb : hg19, version 1.0, accessed March 2026
cscd : hg38, version 2.0, accessed January 2026
exorbase : hg38, version 1.0, accessed May 2026
FASTA
arraystar : hg19, version 2.0, accessed January 2025
circbank : hg19, version 1.0, accessed January 2026
circbase : hg19, version 1.0, accessed January 2026
circpedia : hg38, version 3.0, accessed October 2025
circrnadb : hg19, version 1.0, accessed March 2026
cscd : hg38, version 2.0, accessed January 2026
miRNA
circnet : hg19, version 2.0, accessed January 2026
cscd : hg38, version 2.0, accessed January 2026
RBP
cscd : hg38, version 2.0, accessed January 2026

Mapping Statistics
------------------------------
Annotation
arraystar [270/1000] 27.0%
circRNADb [552/1000] 55.2%
circatlas [939/1000] 93.9%
circbank [950/1000] 95.0%
circbase [458/1000] 45.8%
circpedia [861/1000] 86.1%
cscd [958/1000] 95.8%
exorbase [762/1000] 76.2%

FASTA
arraystar [270/1000] 27.0%
circRNADb [552/1000] 55.2%
circbank [950/1000] 95.0%
circbase [458/1000] 45.8%
circpedia [861/1000] 86.1%
cscd [958/1000] 95.8%

miRNA
chr10 [40/1000] 4.0%
chr11 [46/1000] 4.6%
chr12 [44/1000] 4.4%
chr13 [23/1000] 2.3%
chr14 [29/1000] 2.9%
chr15 [40/1000] 4.0%
chr16 [37/1000] 3.7%
chr17 [41/1000] 4.1%
chr18 [24/1000] 2.4%
chr19 [21/1000] 2.1%
chr1 [93/1000] 9.3%
chr20 [24/1000] 2.4%
chr21 [10/1000] 1.0%
chr22 [11/1000] 1.1%
chr2 [94/1000] 9.4%
chr3 [56/1000] 5.6%
chr4 [57/1000] 5.7%
chr5 [56/1000] 5.6%
chr6 [44/1000] 4.4%
chr7 [56/1000] 5.6%
chr8 [44/1000] 4.4%
chr9 [51/1000] 5.1%
chrX [23/1000] 2.3%

RBP
chr10 [40/1000] 4.0%
chr11 [46/1000] 4.6%
chr12 [44/1000] 4.4%
chr13 [23/1000] 2.3%
chr14 [29/1000] 2.9%
chr15 [40/1000] 4.0%
chr16 [37/1000] 3.7%
chr17 [41/1000] 4.1%
chr18 [24/1000] 2.4%
chr19 [21/1000] 2.1%
chr1 [93/1000] 9.3%
chr20 [24/1000] 2.4%
chr21 [10/1000] 1.0%
chr22 [10/1000] 1.0%
chr2 [94/1000] 9.4%
chr3 [56/1000] 5.6%
chr4 [57/1000] 5.7%
chr5 [55/1000] 5.5%
chr6 [44/1000] 4.4%
chr7 [56/1000] 5.6%
chr8 [44/1000] 4.4%
chr9 [51/1000] 5.1%
chrX [23/1000] 2.3%
24 changes: 0 additions & 24 deletions benchmarks/performance/results/bench_10000/execution_report_2026-08-20_20-04-22.txt
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135 changes: 135 additions & 0 deletions benchmarks/performance/results/bench_10000/execution_report_2026-09-03_12-56-19.txt
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pycircdb execution report
========================================
Timestamp : 2026-09-03 12:56:19
pycircdb version : 1.0.1
Database version : 1.0
Config file : /home/barry/Desktop/pycircdb/benchmarks/performance/configs/bench_10000.json

Global Parameters
--------------------
max_tasks: 1
output_dir: benchmarks/performance/results/bench_10000
tmp_dir: tmp

Samples
--------------------
bench_10000:
file_path : benchmarks/performance/inputs/bench_10000.txt
reference : hg19

Databases & Algorithms
--------------------
Annotation databases : arraystar, circatlas, circbank, circbase, circpedia, circrnadb, cscd, exorbase
FASTA databases : arraystar, circbank, circbase, circpedia, circrnadb, cscd
miRNA algorithms : miRanda, PITA, TargetScan

Database Provenance
--------------------
Annotation
arraystar : hg19, version 2.0, accessed January 2025
circatlas : hg38, version 3.0, accessed January 2026
circbank : hg19, version 1.0, accessed January 2026
circbase : hg19, version 1.0, accessed January 2026
circpedia : hg38, version 3.0, accessed October 2025
circrnadb : hg19, version 1.0, accessed March 2026
cscd : hg38, version 2.0, accessed January 2026
exorbase : hg38, version 1.0, accessed May 2026
FASTA
arraystar : hg19, version 2.0, accessed January 2025
circbank : hg19, version 1.0, accessed January 2026
circbase : hg19, version 1.0, accessed January 2026
circpedia : hg38, version 3.0, accessed October 2025
circrnadb : hg19, version 1.0, accessed March 2026
cscd : hg38, version 2.0, accessed January 2026
miRNA
circnet : hg19, version 2.0, accessed January 2026
cscd : hg38, version 2.0, accessed January 2026
RBP
cscd : hg38, version 2.0, accessed January 2026

Mapping Statistics
------------------------------
Annotation
arraystar [2850/10000] 28.5%
circRNADb [5431/10000] 54.3%
circatlas [9495/10000] 95.0%
circbank [9594/10000] 95.9%
circbase [4664/10000] 46.6%
circpedia [8579/10000] 85.8%
cscd [9628/10000] 96.3%
exorbase [7752/10000] 77.5%

Multi-Mappers
circpedia
hg19:
- chr1:145015859-145021167|-
- chr1:206566045-206567030|+
- chr9:70863721-70875912|+
cscd
hg19:
- chr1:206566045-206567030|+
exorbase
hg19:
- chr1:206566045-206567030|+
- chr9:70863721-70875912|+
- chr9:70863721-70875917|+

FASTA
arraystar [2850/10000] 28.5%
circRNADb [5431/10000] 54.3%
circbank [9594/10000] 95.9%
circbase [4664/10000] 46.6%
circpedia [8583/10000] 85.8%
cscd [9629/10000] 96.3%

miRNA
chr10 [458/10000] 4.6%
chr11 [382/10000] 3.8%
chr12 [501/10000] 5.0%
chr13 [245/10000] 2.5%
chr14 [314/10000] 3.1%
chr15 [414/10000] 4.1%
chr16 [295/10000] 3.0%
chr17 [410/10000] 4.1%
chr18 [239/10000] 2.4%
chr19 [234/10000] 2.3%
chr1 [1001/10000] 10.0%
chr20 [191/10000] 1.9%
chr21 [103/10000] 1.0%
chr22 [161/10000] 1.6%
chr2 [930/10000] 9.3%
chr3 [657/10000] 6.6%
chr4 [500/10000] 5.0%
chr5 [554/10000] 5.5%
chr6 [490/10000] 4.9%
chr7 [578/10000] 5.8%
chr8 [384/10000] 3.8%
chr9 [443/10000] 4.4%
chrX [200/10000] 2.0%
chrY [1/10000] 0.0%

RBP
chr10 [456/10000] 4.6%
chr11 [382/10000] 3.8%
chr12 [500/10000] 5.0%
chr13 [245/10000] 2.5%
chr14 [312/10000] 3.1%
chr15 [411/10000] 4.1%
chr16 [293/10000] 2.9%
chr17 [410/10000] 4.1%
chr18 [239/10000] 2.4%
chr19 [233/10000] 2.3%
chr1 [997/10000] 10.0%
chr20 [190/10000] 1.9%
chr21 [103/10000] 1.0%
chr22 [161/10000] 1.6%
chr2 [930/10000] 9.3%
chr3 [656/10000] 6.6%
chr4 [498/10000] 5.0%
chr5 [553/10000] 5.5%
chr6 [489/10000] 4.9%
chr7 [576/10000] 5.8%
chr8 [381/10000] 3.8%
chr9 [442/10000] 4.4%
chrX [200/10000] 2.0%
chrY [1/10000] 0.0%
24 changes: 0 additions & 24 deletions benchmarks/performance/results/bench_100k/execution_report_2026-08-20_20-05-04.txt
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