pig QTLdb: GFF3 file violates the spec.

[arnikz]

Some required values/columns are missing in the GFF distribution. As a result, there are lines with less than nine columns, which makes parsing more challenging.

(Pathological) example:

Chr.17  Animal QTLdb    Reproduction_QTL     61830469   61855765     QTL_ID=8814;Name=Teat number;Abbrev=TNUM;PUBMED_ID=22443659;trait_ID=167;trait=Teat number;breed=large white,meishan;FlankMarkers;VTO_name=nipple quantity;CMO_name=teat number;Map_Type=Linkage;Model=Mendelian;Test_Base=Genome-wise;peak_cM=85.9;Significance=Significant;P-value=<0.05;Likelihood_Ratio=67.2

Contact the team/helpdesk.

[arnikz]

After all, the GFF file has the required (fixed) number of columns in all lines; the example above was copy/paste error. However, there were a couple of lines without start and end coordinates and are now fixed by the data provider.

[arnikz]

It seems that In the updated GFF distribution there are still 127 feature lines without start/end coordinates. Work in progress...

[arnikz]

Here is the list of QTL IDs:
107253,107254,107255,107256,37847,37610,37611,37612,37613,37614,37615,37616,37617,37618,37619,37620,57634,107257,107258,107259,107268,101475,101528,107269,95893,95923,38083,56250,107240,107245,107248,57638,106314,106315,106316,106317,106318,106319,106320,106321,107260,107270,71077,71078,71079,71080,71081,71082,71083,71084,71085,62295,107241,107246,107249,38056,107250,107261,107262,95943,95944,95945,95946,95947,95948,95949,106201,106202,106203,106204,106205,106206,106207,37672,37705,37733,37744,38063,38065,95950,106287,106414,106415,107263,101780,101786,101790,101805,101817,101846,101858,101878,101890,101905,101907,101914,101919,101934,101941,101414,101440,101451,101476,101485,101517,101529,101543,101744,101778,106288,106289,106290,106291,107251,107252,107264,107265,60828,64663,107242,107243,107244,107247,95951,95952,107266,107267