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Juke34 / RAIN Public

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New pluviometer#46

Merged

eascarrunz merged 57 commits intomainJuke34/RAIN:mainfrom

new-pluviometerJuke34/RAIN:new-pluviometerCopy head branch name to clipboard

Jul 18, 2025

Conversation Commits57 (57)Checks Files changed

Merged

New pluviometer#46
eascarrunz merged 57 commits intomainfrom
new-pluviometer

Commits

Commits on Jul 8, 2025

new pluviometer working
eascarrunz
committed
script rewrite (pluvi.py) + refactoring of other files
eascarrunz
committed
fix progress bar option
eascarrunz
committed

Commits on Jul 10, 2025

replace old pluviometer
eascarrunz
committed
add shebang
eascarrunz
committed
display progress bar
eascarrunz
committed
change permissions to make script executable
eascarrunz
committed
print field with type of parent feature
eascarrunz
committed

Commits on Jul 11, 2025

add logging for record switching
eascarrunz
committed
set pluviometer error strategy to "terminate"
eascarrunz
committed
fix logging that used an attribute that was not set yet
eascarrunz
committed
set logging format, add logging points for GFF parsing
eascarrunz
committed
Aggregate level-1 features selecting only one representative transcript-like feature (longest CDS or greatest total exon length)
eascarrunz
committed
get last position from record's sequence length
eascarrunz
committed
fix last commit
eascarrunz
committed
remove incorrect assertion in `SeqFeature.get_transcript_like`
eascarrunz
committed
disable logging format
eascarrunz
committed
fix typo
eascarrunz
committed
set logging file
eascarrunz
committed
fix logging format string
eascarrunz
committed
add more logging
eascarrunz
committed
correct log messages
eascarrunz
committed
complete level-1 aggregation
eascarrunz
committed
add missing comma in aggregate output field list
eascarrunz
committed
fix output paths
eascarrunz
committed
method for flushing action queue
eascarrunz
committed
make pluviometer.log the base log file name
eascarrunz
committed
add log file to process outputs
eascarrunz
committed
Stop counting when svdata.seqid != self.record.id, and retain the svdata state between records
eascarrunz
committed
fix log file extension (.tsv -> .log)
eascarrunz
committed
initialize svdata (as None)
eascarrunz
committed

Commits on Jul 15, 2025

make readers seek the next entry matching the current record
eascarrunz
committed
open input file for each record
eascarrunz
committed
log hits in seek_record methods
eascarrunz
committed
more logging
eascarrunz
committed
increase waiting time and memory for pluviometer.py
eascarrunz
committed

Commits on Jul 16, 2025

create chimaeric transcripts
eascarrunz
committed
fix typing after name change
eascarrunz
committed
fix missing output field from method `write_row_without_data`
eascarrunz
committed
add parent path to output files
eascarrunz
committed
remove input format comment from output
eascarrunz
committed
old code cleanup
eascarrunz
committed

Commits on Jul 17, 2025

add chromosome and total aggregation tallies
eascarrunz
committed
Perish the aggregation "mode"
eascarrunz
committed
write chromosome totals
eascarrunz
committed
use np.int64 to avoid overflows when computing totals
eascarrunz
committed
code cleanup
eascarrunz
committed
log only one message in the `make_chimaera` method
eascarrunz
committed
remove unnecessary log message
eascarrunz
committed
delete vestige of `mode` parameter
eascarrunz
committed
bug fix: representative transcript selection was checking for type "cds" instead of "CDS"
eascarrunz
committed
improve logging message
eascarrunz
committed

Commits on Jul 18, 2025

parallelization
eascarrunz
committed
set up threads parameter in nf module
eascarrunz
committed
update pluviometer conda env to add natsort
eascarrunz
committed
typo in cpus param
eascarrunz
committed
remove delete before create
eascarrunz
committed

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