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flatfile-to-json.pl show a warning if --trackLabel contains an illegal character #1023

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dytk2134 opened this Issue Mar 14, 2018 · 1 comment

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@dytk2134

dytk2134 commented Mar 14, 2018

Hi,

I was working on adding tracks data to jbrowse by running the flatfile-to-json.pl script. I just wondering if flatfile-to-json.pl can show a warning/error when --trackLable contains an illegal character like slash.

Here is the example command I used:

perl /bin/flatfile-to-json.pl \
--gff /data/ImmunoDB_JAKSTATs.gff3 \
--arrowheadClass trellis-arrowhead \
--getSubfeatures \
--subfeatureClasses '{ "match_part" : "blast-match_part"}' \
--cssClass container-16px \
--type match_part \
--trackLabel "ImmunoDB JAK/STAT pathway proteins tBLASTN" \
--key "ImmunoDB JAK/STAT pathway proteins tBLASTN" \
--config '{ "category": "2. tBlastn" , "metadata": {"Analysis Method" : "tblastn ncbi-blast-2.2.31+"}}'

It seems like the script will try to generate a directory in tracks/ named "ImmunoDB JAK/STAT pathway proteins tBLASTN" and the urlTemplate will also point to that directory.
urlTemplate in trackList.json

"urlTemplate" : "tracks/ImmunoDB JAK/STAT pathway proteins tBLASTN/{refseq}/trackData.json",

However, it failed but generated a directory structure like this:

|-- ImmunoDB JAK
     `--  STAT pathway proteins tBLASTN
            |-- NW_007518467.1
            |-- NW_007515667.1     

Therefore, the jbrowse can't found the tracks data.

Thank you!

@rbuels rbuels added this to the 1.13.1 milestone Mar 14, 2018

@cmdcolin

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cmdcolin commented Mar 23, 2018

If slash is only thing that causes problems, then maybe error and exit from flatfile-to-json like this code: https://github.com/GMOD/jbrowse/tree/warn_slashes

@rbuels rbuels changed the title from flatfile-to-json.pl show a warning if --trackLable contains an illegal character to flatfile-to-json.pl show a warning if --trackLabel contains an illegal character Mar 23, 2018

@rbuels rbuels closed this in bc28540 Mar 23, 2018

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