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Jb2 295 #269

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merged 2 commits into from
Feb 3, 2025
Merged

Jb2 295 #269

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0382135
changing visible instances of gei11 to snpc4. Addresses https://githu…
scottcain Dec 3, 2024
aa1e5fe
hacking to skip extra rnaseq splice configs
scottcain Feb 3, 2025
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7 changes: 6 additions & 1 deletion jbrowse2/bin/make_tracks_config.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -63,11 +63,16 @@

my $includedir = "$Bin/../config/track_configs";

my $seenRNASeq = 0;
for my $f (@includes) {
local $/ = undef;
if (!-e "$includedir/$f") {
warn "$includedir/$f not found\n";
next;
next;
}
if ($f =~ "rnaseq_splice") {
next if ($seenRNASeq);
$seenRNASeq++;
}
open (my $F, "<", "$includedir/$f") or die "$!:$f";
my $data = <$F>;
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42 changes: 21 additions & 21 deletions jbrowse2/config/track_configs/c_elegans_PRJNA13758_modencode2_with_peaks.json
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Original file line number Diff line number Diff line change
Expand Up @@ -12624,7 +12624,7 @@
}
},
{
"name" : "GEI-11 Combined (GFP ChIP), GEI-11_Emb w peaks",
"name" : "SNPC-4 Combined (GFP ChIP), GEI-11_Emb w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
Expand Down Expand Up @@ -12653,7 +12653,7 @@
]
},
{
"description" : "Peak calls for GEI-11 Combined (GFP ChIP), GEI-11_Emb w peaks",
"description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI-11_Emb w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
Expand All @@ -12673,7 +12673,7 @@
}
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI-11_Emb w peaks_bigbed_peaks",
"name" : "__GEI-11 Combined (GFP ChIP), GEI-11_Emb peaks",
"name" : "__SNPC-4 Combined (GFP ChIP), GEI-11_Emb peaks",
"type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
Expand Down Expand Up @@ -12713,10 +12713,10 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"name" : "GEI-11 Combined (GFP ChIP), GEI11_L2_GFP w peaks"
"name" : "SNPC-4 Combined (GFP ChIP), GEI11_L2_GFP w peaks"
},
{
"name" : "__GEI-11 Combined (GFP ChIP), GEI11_L2_GFP peaks",
"name" : "__SNPC-4 Combined (GFP ChIP), GEI11_L2_GFP peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
Expand All @@ -12728,7 +12728,7 @@
},
"type" : "BigBedAdapter"
},
"description" : "Peak calls for GEI-11 Combined (GFP ChIP), GEI11_L2_GFP w peaks",
"description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI11_L2_GFP w peaks",
"displays" : [
{
"type" : "LinearBasicDisplay",
Expand All @@ -12750,7 +12750,7 @@
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI11_L2_GFP w peaks_bigbed_peaks"
},
{
"name" : "GEI-11 Combined (GFP ChIP), GEI11_L3_GFP w peaks",
"name" : "SNPC-4 Combined (GFP ChIP), GEI11_L3_GFP w peaks",
"type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
Expand Down Expand Up @@ -12779,7 +12779,7 @@
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI11_L3_GFP w peaks"
},
{
"description" : "Peak calls for GEI-11 Combined (GFP ChIP), GEI11_L3_GFP w peaks",
"description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI11_L3_GFP w peaks",
"displays" : [
{
"displayId" : "GEI-11 Combined (GFP ChIP)_ GEI11_L3_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
Expand All @@ -12803,7 +12803,7 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"name" : "__GEI-11 Combined (GFP ChIP), GEI11_L3_GFP peaks",
"name" : "__SNPC-4 Combined (GFP ChIP), GEI11_L3_GFP peaks",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
Expand All @@ -12817,7 +12817,7 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"name" : "GEI-11 Combined (GFP ChIP), GEI11_L4_GFP w peaks",
"name" : "SNPC-4 Combined (GFP ChIP), GEI11_L4_GFP w peaks",
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
Expand Down Expand Up @@ -12861,15 +12861,15 @@
"Transcription Factors",
"GFP ChIP"
],
"description" : "Peak calls for GEI-11 Combined (GFP ChIP), GEI11_L4_GFP w peaks",
"description" : "Peak calls for SNPC-4 (GEI-11) Combined (GFP ChIP), GEI11_L4_GFP w peaks",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4360_details.gff.bb",
"locationType" : "UriLocation"
}
},
"name" : "__GEI-11 Combined (GFP ChIP), GEI11_L4_GFP peaks",
"name" : "__SNPC-4 Combined (GFP ChIP), GEI11_L4_GFP peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
Expand Down Expand Up @@ -12902,22 +12902,22 @@
"c_elegans_PRJNA13758"
],
"type" : "QuantitativeTrack",
"name" : "GEI-11 Combined (GFP ChIP), GEI-11_L1 w peaks"
"name" : "SNPC-4 Combined (GFP ChIP), GEI-11_L1 w peaks"
},
{
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"type" : "FeatureTrack",
"name" : "__GEI-11 Combined (GFP ChIP), GEI-11_L1 peaks",
"name" : "__SNPC-4 Combined (GFP ChIP), GEI-11_L1 peaks",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18819_details.gff.bb"
}
},
"description" : "Peak calls for GEI-11 Combined (GFP ChIP), GEI-11_L1 w peaks",
"description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI-11_L1 w peaks",
"displays" : [
{
"displayId" : "GEI-11 Combined (GFP ChIP)_ GEI-11_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
Expand Down Expand Up @@ -12954,7 +12954,7 @@
"Transcription Factors",
"GFP ChIP"
],
"name" : "GEI-11 Combined (GFP ChIP), GEI-11_YA w peaks",
"name" : "SNPC-4 Combined (GFP ChIP), GEI-11_YA w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
Expand All @@ -12972,7 +12972,7 @@
"c_elegans_PRJNA13758"
],
"type" : "FeatureTrack",
"name" : "__GEI-11 Combined (GFP ChIP), GEI-11_YA peaks",
"name" : "__SNPC-4 Combined (GFP ChIP), GEI-11_YA peaks",
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18904_details.gff.bb",
Expand All @@ -12981,7 +12981,7 @@
"type" : "BigBedAdapter"
},
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI-11_YA w peaks_bigbed_peaks",
"description" : "Peak calls for GEI-11 Combined (GFP ChIP), GEI-11_YA w peaks",
"description" : "Peak calls for SNPC-4 (GEI-11) Combined (GFP ChIP), GEI-11_YA w peaks",
"displays" : [
{
"type" : "LinearBasicDisplay",
Expand Down Expand Up @@ -14921,7 +14921,7 @@
}
},
{
"name" : "GEI-11 Combined (GFP ChIP) recalled peaks w peaks",
"name" : "SNPC-4 Combined (GFP ChIP) recalled peaks w peaks",
"type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
Expand Down Expand Up @@ -14950,7 +14950,7 @@
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_GEI-11 Combined (GFP ChIP) recalled peaks w peaks"
},
{
"name" : "__GEI-11 Combined (GFP ChIP) recalled peaks peaks",
"name" : "__SNPC-4 Combined (GFP ChIP) recalled peaks peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
Expand All @@ -14962,7 +14962,7 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8063_details.gff.bb"
}
},
"description" : "Peak calls for GEI-11 Combined (GFP ChIP) recalled peaks w peaks",
"description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP) recalled peaks w peaks",
"displays" : [
{
"type" : "LinearBasicDisplay",
Expand Down