fix_partial_CDS function implemented
Fix pseudo-partial CDS predicted at the end of the contig, but is likely to be intact.
The one that meet the following conditions will be retained as a misc_feature or a intact CDS.
- Starts at the coordinate 1 (+ strand) or at the end of contig (- strand)
- 5'-end is missing and 3'-end is intact (+ strand) or the opposite case (- strand)
- length is multiple of 3 and > min_length
- the CDS has significant protein hit
For CDS on + strand,
partial_flag 10, strand +, len>=500
For CDS on - strand
partial_flag 01, strand -, len>=500
if the first 3 nuleotides are in [ATG, GTG, TTG], the CDS is fixed as intact. Otherwise, it is annotated as misc_feature.
- Added output for the summary of pseudogene detection
- Fixed bug in PseudogeneDetection when transl_except is found in the fragmented contig.
transl_except will be ignored when insertion/deletion/stop_cond is found in the same alignment.
- Fixed bug in automatic DB indexing when .pal file exists
v.1.2.6: Added options to enable GeneMarkS2, Diamond, RNAmmer
Added options to enable GeneMarkS2, Diamond, RNAmmer
As per the pull request #25 and the issue #20, command-line options to enable GeneMarkS2, Diamond, RNAmmer have been added.
See FAQ for more details.
--aligner STR Aligner to use [ghostx(=default)|blastp|diamond] --use_genemarks2 STR Use GeneMarkS2 to predict CDS instead of MGA. [auto|bact|arch] --use_rnammer STR Use RNAmmer to predict rRNA instead of Barrnap. [bact|arch]
Note that GeneMarkS2, Diamond, RNAmmer are not bundled in the software package. If you want to use them, please install them by yourself.
Thank @AaronRuben for the PR for GeneMarkS2!