| 129 |
|
bool fullCDSonly=false; // starts with START, ends with STOP codon |
| 130 |
|
bool fullattr=false; |
| 131 |
|
//bool sortByLoc=false; // if the GFF output should be sorted by location |
| 132 |
< |
bool ensembl_convert=false; //-L, assisst in converting Ensembl GTF to GFF3 |
| 132 |
> |
bool ensembl_convert=false; //-L, assist in converting Ensembl GTF to GFF3 |
| 133 |
|
|
| 134 |
|
|
| 135 |
|
//GStr gseqpath; |
| 309 |
|
if (gname==NULL) gname=gffrec.getGeneID(); |
| 310 |
|
GStr defline(gffrec.getID()); |
| 311 |
|
if (f_out && !fmtGTF) { |
| 312 |
< |
const char* tn=NULL; |
| 313 |
< |
if ((tn=gffrec.getAttr("transcript_name"))!=NULL) { |
| 314 |
< |
gffrec.addAttr("Name", tn); |
| 312 |
> |
const char* tname=NULL; |
| 313 |
> |
if ((tname=gffrec.getAttr("transcript_name"))!=NULL) { |
| 314 |
> |
gffrec.addAttr("Name", tname); |
| 315 |
|
gffrec.removeAttr("transcript_name"); |
| 316 |
|
} |
| 317 |
|
} |
| 318 |
|
if (ensembl_convert && startsWith(gffrec.getID(), "ENS")) { |
| 319 |
< |
const char* tn=gffrec.getTrackName(); |
| 320 |
< |
gffrec.addAttr("type", tn); |
| 319 |
> |
const char* biotype=gffrec.getAttr("gene_biotype"); |
| 320 |
> |
if (biotype) { |
| 321 |
> |
gffrec.addAttr("type", biotype); |
| 322 |
> |
gffrec.removeAttr("gene_biotype"); |
| 323 |
> |
} |
| 324 |
> |
else { //old Ensembl files lacking gene_biotype |
| 325 |
> |
gffrec.addAttr("type", gffrec.getTrackName()); |
| 326 |
> |
} |
| 327 |
> |
|
| 328 |
|
//bool is_gene=false; |
| 329 |
|
bool is_pseudo=false; |
| 330 |
< |
if (strcmp(tn, "protein_coding")==0 || gffrec.hasCDS()) |
| 330 |
> |
if (strcmp(biotype, "protein_coding")==0 || gffrec.hasCDS()) |
| 331 |
|
gffrec.setFeatureName("mRNA"); |
| 332 |
|
else { |
| 333 |
< |
if (strcmp(tn, "processed_transcript")==0) |
| 333 |
> |
if (strcmp(biotype, "processed_transcript")==0) |
| 334 |
|
gffrec.setFeatureName("proc_RNA"); |
| 335 |
|
else { |
| 336 |
< |
//is_gene=endsWith(tn, "gene"); |
| 337 |
< |
is_pseudo=strifind(tn, "pseudo"); |
| 336 |
> |
//is_gene=endsWith(biotype, "gene"); |
| 337 |
> |
is_pseudo=strifind(biotype, "pseudo"); |
| 338 |
|
if (is_pseudo) { |
| 339 |
|
gffrec.setFeatureName("pseudo_RNA"); |
| 340 |
|
} |
| 341 |
< |
else if (endsWith(tn, "RNA")) { |
| 342 |
< |
gffrec.setFeatureName(tn); |
| 341 |
> |
else if (endsWith(biotype, "RNA")) { |
| 342 |
> |
gffrec.setFeatureName(biotype); |
| 343 |
|
} else gffrec.setFeatureName("misc_RNA"); |
| 344 |
|
} |
| 345 |
|
} |
