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Bigbed to gtf converter and tests #19809

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Bigbed to gtf converter and tests #19809

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3290f7f
bigbed to gtf converter w tests
d-callan Mar 12, 2025
edc7aa6
clean up output gtf some for bigbedtogtf converter
d-callan Mar 13, 2025
94d38d2
simplify bigbedtogtf converter some
d-callan Mar 13, 2025
92f3f27
bigbed to gtf converter w tests
d-callan Mar 12, 2025
4a9794a
clean up output gtf some for bigbedtogtf converter
d-callan Mar 13, 2025
ddbda74
simplify bigbedtogtf converter some
d-callan Mar 13, 2025
0ac9afa
Merge branch 'bigbed-to-gtf-converter' of github.com:d-callan/galaxy …
d-callan Mar 19, 2025
e8ab1cf
improve bigbed to gtf converter tests
d-callan Mar 19, 2025
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clean up output gtf some for bigbedtogtf converter
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@d-callan
d-callan committed Mar 13, 2025
commit edc7aa6b38c8623f1c3aa74344d2d8b7641210e1
4 changes: 2 additions & 2 deletions lib/galaxy/datatypes/converters/bigbed_to_gtf_converter.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="ucsc_bigbedtogtf" name="Convert from bigBed to GTF format" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
<tool id="bigbedtogtf" name="Convert from bigBed to GTF format" version="@TOOL_VERSION@+galaxy@SUFFIX_VERSION@" profile="20.01">
<description>Convert bigBed to GTF</description>
<macros>
<token name="@TOOL_VERSION@">377</token>
Expand Down Expand Up @@ -26,7 +26,7 @@
python '$__tool_directory__/bed_to_gff_converter.py' temp.bed temp.gff &&
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Is there a reason you're not using genePredToGtf ? I don't know if we can trust that 17 year old hand-written bed to gff script ...

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i was partly trying to be consistent w what was already here. it seemed to me like itd be unexpected as a user if i got a very different gtf vs gff2 file w the same input. but also, i was a little worried that if the incoming file wasnt from ucsc that the genepred intermediate file wouldnt make sense or maybe even work. (im not really confident i know what genepred is tbh) and if we did know the incoming data was from ucsc, why not have a genepred to gtf converter?

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Agree these are issues, but realistically I think all bigbeds come from ucsc. That said, I think the bigbed to bed converter was the important one that would have an application, maybe we can wait until there's a reason not to use the pre-built gtfs hosted by ucsc before we proceed here ? If there is an actual application we'll also know if this will all work out correctly.


## Step 3: Convert GFF to GTF (GFF2 is very similar to GTF, just need to adjust the last column)
awk -F '\t' '{
awk -F '\t' 'NR > 3 && $1 !~ /^#/ {
if ($1 !~ /^#/) {
split($9, attrs, ";");
feature_id = "";
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3 changes: 0 additions & 3 deletions test-data/output.gtf
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@@ -1,6 +1,3 @@
##gff-version 2
##bed_to_gff_converter.py
gene_id "gene___"; transcript_id "gene___";
chr7 bed2gff uc003sii.2 54029 73584 0 - . gene_id "gene_chr7_54029_73584"; transcript_id "gene_chr7_54029_73584";
chr7 bed2gff uc010krx.1 60329 61569 0 - . gene_id "gene_chr7_60329_61569"; transcript_id "gene_chr7_60329_61569";
chr7 bed2gff uc003sij.2 62968 63529 0 - . gene_id "gene_chr7_62968_63529"; transcript_id "gene_chr7_62968_63529";
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