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dcjones / isolator

Rapid and robust analysis of RNA-Seq experiments.
MIT License
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Cryptic "Error parsing YAML file" #2

Closed petercombs closed 7 years ago

petercombs commented 7 years ago

Hi, I'm interested in running Isolator on my data (which has thus far been resistant to other splicing analyzers; I'm willing to believe there are no interesting splicing differences, though). However, it gives me an error when I try to run it:

$ ls SB30/assigned_dmelR.bam
    SB30/assigned_dmelR.bam
$ isolator analyze ~/HybridSliceSeq/Reference/mel_r5_good.gtf ~/HybridSliceSeq/tmp/isolator_small.yaml
 Version: 0.0.2-102-g24bafc0
 Instruction set: SSE4

[15:41:00] 2489 cassette exons
[15:41:01] 1549 retained introns
[15:41:01] Error parsing YAML file /home/pcombs/HybridSliceSeq/tmp/isolator_small.yaml

The file I'm using is: 

sim_chunk01:
        sim_sl01: SB33/assigned_dmelR.bam
        sim_sl03: SB31/assigned_dmelR.bam
        sim_sl02: SB32/assigned_dmelR.bam

sim_chunk02:
        sim_sl05: SB29/assigned_dmelR.bam
        sim_sl06: SB28/assigned_dmelR.bam
        sim_sl04: SB30/assigned_dmelR.bam

with each sample (SB28-33) in its own directory. Is putting each sample in its own directory not valid? Is there something else I'm doing that's obviously wrong?

petercombs commented 7 years ago

Some further digging suggests that the issue was using tab characters instead of spaces. After poring through the YAML spec even more deeply than yesterday (6.1: "To maintain portability, tab characters must not be used in indentation"), I believe throwing a parse error is the correct behavior.