[Gmod-ajax] autocompletion

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[Gmod-ajax] autocompletion

Ke Jiang
Hi,

For some genomes and their annotations, I could load GFF3 and display them properly, as well as run generate-names.pl without any errors. The generated name index also looked fine, but I was unable to see auto-completion in the search window. I double-checked the GFF3 files and indices, they both looked perfectly normal (see below). Would anyone suggest some possible causes? The only difference with these genomes is that they consist of over 10,000 contigs or scaffolds. Is this something related to the indexing problem?

Sample GFF3

Scaffold4       I5K     gene    342996  344681  .       -       .       ID=HHAL000001;Name=Dmel-Tmp-kek1;Alias="KEK1";Dbxref=i5kP_homolog_HSAPI:ENSP00000249363;Dbxref=i5kP_homolog_HSAPI:ENSP00000278198;Dbxref=i5kP_homolog_HSAPI:ENSP00000373853;Dbxref=i5kP_homolog_MMUSC:ENSMUSP00000053123;Dbxref=i5kP_homolog_MMUSC:ENSMUSP00000062158;Dbxref=i5kP_homolog_MMUSC:ENSMUSP00000130984;Dbxref=i5kP_homolog_AGAMB:AGAP009136-PA;Dbxref=i5kP_homolog_AMEL:GB40751-PA;Dbxref=i5kP_homolog_BMORI:BGIBMGA010659-PA;Dbxref=i5kP_homolog_DMELA:FBpp0304518;Dbxref=i5kP_homolog_TCAST:TC007055;
Scaffold4       I5K     mRNA    342996  344681  .       -       .       ID=HHAL000001-RA;Name=HhalTmpA000001-RA;Parent=HHAL000001;Dbxref=Pfam:PF00560;Dbxref=Pfam:PF07679;Dbxref=SMART:SM00369;Dbxref=Pfam:PF13855;Dbxref=SUPERFAMILY:SSF52058;Dbxref=ProSiteProfiles:PS51450;Dbxref=ProSiteProfiles:PS50835;Dbxref=Gene3D:G3DSA:2.60.40.10;Dbxref=SMART:SM00082;Dbxref=SMART:SM00409;Dbxref=Gene3D:G3DSA:3.80.10.10;Dbxref=SMART:SM00408;Dbxref=SUPERFAMILY:SSF48726;
Scaffold4       I5K     exon    342996  344681  .       -       .       ID=HHAL000001-RA-EXON01;Parent=HHAL000001-RA;
Scaffold4       I5K     CDS     342996  344681  .       -       0       ID=HHAL000001-RA-CDS01;Parent=HHAL000001-RA;

Sample index

{"\"lp0715":{"exact":[],"prefix":["\"LP07155p\""]},"scaffold10116":{"exact":[["Scaffold10116",6168,"Scaffold10116",null,0,6168,20000]],"prefix":[]},"dmel-tmp-are":{"exact":[],"prefix":["Dm
el-Tmp-aret"]},"\"ld47606p":{"exact":[],"prefix":["\"LD47606p\""]},"hhal006225":{"exact":[["HHAL006225",0,"HhalTmpA006225","Scaffold190",566226,567108]],"prefix":[]}

Output from generate-names.pl

Tracks:
    genes
    miRNAs
Sampled input stats:
                   avg record text bytes 16
                      name input records 12168
        operation stream estimated count 954168
           record stream estimated count 79514
                     total namerec bytes 194688
                       total input bytes 1272234
                         operations made 50000
                       namerecs buffered 12168
        namerecs converted to operations 4003
Removing existing contents of target dir data/json/xxxx/names
Hash store cache size: 2684 buckets
Using 1 chars for sort log names (16 sort logs)


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