Mercurial > repos > vipints > fml_mergeloci
diff fml_gff_groomer/t/Feature_ID_mapping_W.txt @ 0:79726c328621 default tip
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
| author | vipints |
|---|---|
| date | Tue, 07 Jun 2011 17:29:24 -0400 |
| parents | |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fml_gff_groomer/t/Feature_ID_mapping_W.txt Tue Jun 07 17:29:24 2011 -0400 @@ -0,0 +1,23 @@ +------------------------------------------------------- +GFFExamine started on Mon Apr 18 13:17:17 2011 +------------------------------------------------------- + +===Report on different level features from GFF file=== + +FIRST level feature(s): + ('Coding_transcript', 'gene') + +SECOND level feature(s): + ('Coding_transcript', 'mRNA') + +THIRD level feature(s): + ('Coding_transcript', 'CDS'), ('Coding_transcript', 'five_prime_UTR'), ('Coding_transcript', 'three_prime_UTR') + +GFF Parsing modules from publicly available packages like Bio-python, Bio-perl etc. are heavily dependent on feature identifier mapping. +Here few features seems to be wrongly mapped to its child, which inturn cause problems while extracting the annotation based on feature identifier. + +Error in ID mapping: Level1 feature ('Coding_transcript', 'gene') maps to Level3 feature ('Coding_transcript', 'exon') +Error in ID mapping: Level1 feature ('Coding_transcript', 'gene') maps to Level3 feature ('Coding_transcript', 'intron') +------------------------------------------------------- +GFFExamine finished at Mon Apr 18 13:17:17 2011 +-------------------------------------------------------