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adding changes made since 289 was released #233

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merged 9 commits into from
Sep 12, 2023
Merged

adding changes made since 289 was released #233

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5352cd3
adding alliance link to curated genes track
scottcain Jul 3, 2023
69c62cc
adding SFU crispr track
scottcain Jul 4, 2023
0a9bd53
adding an option for expanding out fasta info (needs tested still)
scottcain Jul 5, 2023
d0e6edb
adding the set of pattern match tracks
scottcain Jul 5, 2023
f3f67f9
didn't mean to commit this
scottcain Jul 5, 2023
c21a17e
fixing the color plugin for the CeNDR track
scottcain Jul 5, 2023
c6eb8a9
fixing an incorrect assembly
scottcain Aug 23, 2023
5263fb5
Merge branch 'jb2-289' of https://github.com/WormBase/website-genome-…
scottcain Aug 23, 2023
b5bbbd8
adding nigoni synteny tracks
scottcain Aug 23, 2023
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6 changes: 4 additions & 2 deletions jbrowse2/bin/make_tracks_config.pl
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Expand Up @@ -27,6 +27,9 @@
$ASSEMBLY ||= 'c_elegans_PRJNA13758';
$S3URL ||= 'https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase';

my $SEQUENCE = $ASSEMBLY;
$SEQUENCE =~ s/_P/.P/;

#fetch trackList.json, parse into JSON object
# the ".old" json file is the one that has the includes list
# rather than the trackList.json that is used for JB 1, where
Expand Down Expand Up @@ -54,8 +57,6 @@
$i =~ s/includes\///;
push @includes, $i unless ($i =~ /functions.conf/
or $i =~ /PR.*DNA.json/
or $i =~ /pattern_match_tracks/
or $i =~ /crispr_predictions/
or $i =~ /alphafold/
or $i =~ /expression_patterns/);
}
Expand All @@ -77,6 +78,7 @@
#do the substitutions, then json-ify
$data =~ s/\$RELEASE/$RELEASE/g;
$data =~ s/\$ASSEMBLY/$ASSEMBLY/g;
$data =~ s/\$SEQUENCE/$SEQUENCE/g;
my $json = JSON->new->decode($data);

push @tracks, @{$json->{tracks}};
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1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/b_malayi_PRJNA10729_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_angaria_PRJNA51225_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_becei_PRJEB28243_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_bovis_PRJEB34497_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_brenneri_PRJNA20035_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_briggsae_PRJNA10731_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
35 changes: 35 additions & 0 deletions jbrowse2/config/track_configs/c_briggsae_PRJNA10731_synteny.json
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@@ -1,4 +1,39 @@
{"tracks":[
{
"assemblyNames" : [
"c_briggsae_PRJNA10731",
"c_nigoni_PRJNA384657"
],
"displays" : [
{
"displayId" : "briggsae_to_nigoni-DotplotDisplay",
"type" : "DotplotDisplay"
},
{
"displayId" : "briggsae_to_nigoni-LinearComparativeDisplay",
"type" : "LinearComparativeDisplay"
},
{
"displayId" : "briggsae_to_nigoni-LinearSyntenyDisplay",
"type" : "LinearSyntenyDisplay"
}
],
"name" : "C. briggsae to C. nigoni",
"adapter" : {
"type" : "PAFAdapter",
"pafLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_briggsae.c_nigoni.paf"
},
"queryAssembly" : "c_nigoni_PRJNA384657",
"targetAssembly" : "c_briggsae_PRJNA10731"
},
"category" : [
"Synteny"
],
"trackId" : "briggsae_to_nigoni",
"type" : "SyntenyTrack"
},
{
"category": [
"Synteny"
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1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_elegans_PRJEB28388_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
2 changes: 1 addition & 1 deletion jbrowse2/config/track_configs/c_elegans_PRJEB28388_synteny.json
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Expand Up @@ -12,7 +12,7 @@
],
"adapter": {
"type": "PAFAdapter",
"queryAssembly": "c_remanei_PRJNA53967",
"queryAssembly": "c_elegans_PRJEB28388",
"targetAssembly": "c_elegans_PRJNA275000",
"pafLocation": {
"locationType": "UriLocation",
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37 changes: 37 additions & 0 deletions jbrowse2/config/track_configs/c_elegans_PRJNA13758_crispr_predictions.json
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{
"tracks": [
{
"type": "FeatureTrack",
"trackId": "c_elegans_PRJNA13758-crispr_cas9_sgrna_predictions",
"name": "CRISPR_Cas9 sgRNA predictions",
"assemblyNames": [
"c_elegans_PRJNA13758"
],
"description": "sgRNA predictions from http://genome.sfu.ca/crispr/. Used by permission.",
"category": [
"Externally Sourced Resources",
"CRISPR predictions"
],
"adapter": {
"type": "NCListAdapter",
"rootUrlTemplate": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/CRISPR_Cas9 sgRNA predictions/{refseq}/trackData.jsonz"
}
},
"displays": [
{
"type": "LinearBasicDisplay",
"displayId": "crispr_cas9_sgrna_predictions-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer": {
"type": "SvgFeatureRenderer",
"color1": "gold",
"height": 4,
"showLabels": false,
"showDescriptions": false
}
}
]
}
]
}
184 changes: 184 additions & 0 deletions jbrowse2/config/track_configs/c_elegans_PRJNA13758_pattern_match_tracks.json
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{
"tracks": [
{
"type": "FeatureTrack",
"trackId": "$ASSEMBLY_TTCN_sequence_search",
"name": "Cas12e TTCN PAM sites",
"assemblyNames": [
"$ASSEMBLY"
],
"description": "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"category": [
"Externally Sourced Resources",
"CRISPR predictions"
],
"adapter": {
"type": "SequenceSearchAdapter",
"search": "TTC.",
"sequenceAdapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/$SEQUENCE.WS284.genomic.fa.gz"
},
"faiLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/$SEQUENCE.WS284.genomic.fa.gz.fai"
},
"gziLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/$SEQUENCE.WS284.genomic.fa.gz.gzi"
}
}
},
"displays": [
{
"type": "LinearBasicDisplay",
"displayId": "TTCN_sequence_search_$ASSEMBLY-LinearBasicDisplay",
"renderer": {
"type": "SvgFeatureRenderer",
"color1": "SlateBlue",
"height": 4,
"showLabels": false,
"showDescriptions": false
}
}
]
},
{
"type": "FeatureTrack",
"trackId": "$ASSEMBLY_TTN_sequence_search",
"name": "Cas12a TTN PAM sites",
"assemblyNames": [
"$ASSEMBLY"
],
"description": "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"category": [
"Externally Sourced Resources",
"CRISPR predictions"
],
"adapter": {
"type": "SequenceSearchAdapter",
"search": "TT.",
"sequenceAdapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/$SEQUENCE.WS284.genomic.fa.gz"
},
"faiLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/$SEQUENCE.WS284.genomic.fa.gz.fai"
},
"gziLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/$SEQUENCE.WS284.genomic.fa.gz.gzi"
}
}
},
"displays": [
{
"type": "LinearBasicDisplay",
"displayId": "TTN_sequence_search_$ASSEMBLY-LinearBasicDisplay",
"renderer": {
"type": "SvgFeatureRenderer",
"color1": "Indigo",
"height": 4,
"showLabels": false,
"showDescriptions": false
}
}
]
},
{
"type": "FeatureTrack",
"trackId": "$ASSEMBLY_NNGRRT_sequence_search",
"name": "SaCas9 NNGRRT PAM sites",
"assemblyNames": [
"$ASSEMBLY"
],
"description": "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
"category": [
"Externally Sourced Resources",
"CRISPR predictions"
],
"adapter": {
"type": "SequenceSearchAdapter",
"search": "..G[AG][AG]T",
"sequenceAdapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/$SEQUENCE.WS284.genomic.fa.gz"
},
"faiLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/$SEQUENCE.WS284.genomic.fa.gz.fai"
},
"gziLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/$SEQUENCE.WS284.genomic.fa.gz.gzi"
}
}
},
"displays": [
{
"type": "LinearBasicDisplay",
"displayId": "NNGRRT_sequence_search_$ASSEMBLY-LinearBasicDisplay",
"renderer": {
"type": "SvgFeatureRenderer",
"color1": "DarkViolet",
"height": 4,
"showLabels": false,
"showDescriptions": false
}
}
]
},
{
"type": "FeatureTrack",
"trackId": "$ASSEMBLY_NGG_sequence_search",
"name": "SpCas9 NGG PAM sites",
"assemblyNames": [
"$ASSEMBLY"
],
"description": "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"category": [
"Externally Sourced Resources",
"CRISPR predictions"
],
"adapter": {
"type": "SequenceSearchAdapter",
"search": ".GG",
"sequenceAdapter": {
"type": "BgzipFastaAdapter",
"fastaLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/$SEQUENCE.WS284.genomic.fa.gz"
},
"faiLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/$SEQUENCE.WS284.genomic.fa.gz.fai"
},
"gziLocation": {
"locationType": "UriLocation",
"uri": "https://s3.amazonaws.com/wormbase-modencode/fasta/current/$SEQUENCE.WS284.genomic.fa.gz.gzi"
}
}
},
"displays": [
{
"type": "LinearBasicDisplay",
"displayId": "NGG_sequence_search_$ASSEMBLY-LinearBasicDisplay",
"renderer": {
"type": "SvgFeatureRenderer",
"color1": "RebeccaPurple",
"height": 4,
"showLabels": false,
"showDescriptions": false
}
}
]
}
]
}
35 changes: 35 additions & 0 deletions jbrowse2/config/track_configs/c_elegans_PRJNA13758_synteny.json
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Expand Up @@ -35,6 +35,41 @@
}
]
},
{
"adapter" : {
"type" : "PAFAdapter",
"pafLocation" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_elegans.c_nigoni.paf",
"locationType" : "UriLocation"
},
"queryAssembly" : "c_nigoni_PRJNA384657",
"targetAssembly" : "c_elegans_PRJNA13758"
},
"name" : "C. elegans N2 to C. nigoni",
"displays" : [
{
"type" : "DotplotDisplay",
"displayId" : "N2_to_nigoni-DotplotDisplay"
},
{
"type" : "LinearComparativeDisplay",
"displayId" : "N2_to_nigoni-LinearComparativeDisplay"
},
{
"displayId" : "N2_to_nigoni-LinearSyntenyDisplay",
"type" : "LinearSyntenyDisplay"
}
],
"assemblyNames" : [
"c_nigoni_PRJNA384657",
"c_elegans_PRJNA13758"
],
"type" : "SyntenyTrack",
"trackId" : "N2_to_nigoni",
"category" : [
"Synteny"
]
},
{
"category": [
"Synteny"
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1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_elegans_PRJNA275000_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_inopinata_PRJDB5687_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_japonica_PRJNA12591_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_latens_PRJNA248912_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_nigoni_PRJNA384657_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_panamensis_PRJEB28259_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_parvicauda_PRJEB12595_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_quiockensis_PRJEB11354_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_remanei_PRJNA248909_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_remanei_PRJNA248911_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_remanei_PRJNA53967_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
1 change: 1 addition & 0 deletions jbrowse2/config/track_configs/c_remanei_PRJNA577507_pattern_match_tracks.json
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c_elegans_PRJNA13758_pattern_match_tracks.json
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