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YeoLab / outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
http://yeolab.github.io/outrigger/
BSD 3-Clause "New" or "Revised" License
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--output doesn't actually work with `outrigger index` #44

Open olgabot opened 8 years ago

olgabot commented 8 years ago

Specifying an output directory with --output doesn't actually work. It still outputs to outrigger_output/:

$ make arabdopsis
rm -rf arabdopsis_outrigger_output
outrigger index \
        --sj-out-tab outrigger/tests/data/arabdopsis/unprocessed/rna.chr4.SJ.out.tab \
        --gtf outrigger/tests/data/arabdopsis/unprocessed/Arabidopsis_thaliana.TAIR10.31.chr4.gtf \
        --output arabdopsis_outrigger_output
self.junction_reads_csv: None
2016-10-11 14:10:34 Creating folder ./outrigger_output ...
2016-10-11 14:10:34     Done.
2016-10-11 14:10:34 Creating folder ./outrigger_output/index ...
2016-10-11 14:10:34     Done.
2016-10-11 14:10:34 Creating folder ./outrigger_output/index/gtf ...
2016-10-11 14:10:34     Done.
2016-10-11 14:10:34 Creating folder ./outrigger_output/junctions ...
2016-10-11 14:10:34     Done.