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dcjones / proseg

Probabilistic cell segmentation for in situ spatial transcriptomics
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Proseg-to-baysor ParseError("Error while parsing value transcript_id for column 0 at line 0") #31

Closed devianggr closed 2 months ago

devianggr commented 2 months ago

Hi,

I have an issue converting the CSV and geojson files to baysor-compatible files for Xenium Ranger running. The issue that I received, was like this: Parse error-proseg to baysor

I don't know what the problem is in this case. But I hope you could help me solving this issue soon.

Thanks a lot!

Devi

brandenjlynch commented 2 months ago

Seeing the same issue -- the format of my transcripts file, after running proseg, looks like this (subsequent rows omitted): transcript_id,x,y,z,observed_x,observed_y,observed_z,gene,qv,fov,assignment,probability,background,confusion 281500746519737,220.87396,17372.799,16.035217,221.47133,17372.148,13.866151,Hp,11.953445,AA3,4294967295,1.00001,1,0

Command: proseg-to-baysor transcript-metadata.csv.gz cell-polygons.geojson.gz

asmilagswash commented 2 months ago

Seeing the same issue , i would just like to add i dont see any cell column in the transcript-metdata.csv but I think the script needs a "cell" column

came203 commented 2 months ago

Seeing the same issue here, my transcript-metadata.csv.gz looks like:


transcript_id,x,y,z,observed_x,observed_y,observed_z,gene,qv,fov,assignment,probability,background,confusion
0,11133.598,7328.0205,2.3660069,11133.936,7327.5967,0.0,Ngfr,inf,0,17056,0.21,0,1

Command: proseg-to-baysor transcript-metadata.csv.gz cell-polygons.geojson.gz --output-transcript-metadata baysor-transcript-metadata.csv --output-cell-polygons baysor-cell-polygons.geojson

The backtrace gives me the following:


thread 'main' panicked at /home/user/.cargo/registry/src/index.crates.io-6f17d22bba15001f/proseg-1.1.3/src/to_baysor.rs:170:35:
Unable to read record batch.: ParseError("Error while parsing value transcript_id for column 0 at line 0")
stack backtrace:
   0: rust_begin_unwind
   1: core::panicking::panic_fmt
   2: core::result::unwrap_failed
   3: proseg_to_baysor::read_proseg_transcript_metadata
   4: proseg_to_baysor::main
note: Some details are omitted, run with `RUST_BACKTRACE=full` for a verbose backtrace.
dcjones commented 2 months ago

Apologies for the regression introduced here. It's now fixed in version 1.1.4. It should not be necessary to re-run proseg.

brandenjlynch commented 2 months ago

Thank you! I will give it a try now.