Mercurial > repos > vipints > fml_mergeloci
comparison 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 |
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date | Tue, 07 Jun 2011 17:29:24 -0400 |
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-1:000000000000 | 0:79726c328621 |
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1 ------------------------------------------------------- | |
2 GFFExamine started on Mon Apr 18 13:17:17 2011 | |
3 ------------------------------------------------------- | |
4 | |
5 ===Report on different level features from GFF file=== | |
6 | |
7 FIRST level feature(s): | |
8 ('Coding_transcript', 'gene') | |
9 | |
10 SECOND level feature(s): | |
11 ('Coding_transcript', 'mRNA') | |
12 | |
13 THIRD level feature(s): | |
14 ('Coding_transcript', 'CDS'), ('Coding_transcript', 'five_prime_UTR'), ('Coding_transcript', 'three_prime_UTR') | |
15 | |
16 GFF Parsing modules from publicly available packages like Bio-python, Bio-perl etc. are heavily dependent on feature identifier mapping. | |
17 Here few features seems to be wrongly mapped to its child, which inturn cause problems while extracting the annotation based on feature identifier. | |
18 | |
19 Error in ID mapping: Level1 feature ('Coding_transcript', 'gene') maps to Level3 feature ('Coding_transcript', 'exon') | |
20 Error in ID mapping: Level1 feature ('Coding_transcript', 'gene') maps to Level3 feature ('Coding_transcript', 'intron') | |
21 ------------------------------------------------------- | |
22 GFFExamine finished at Mon Apr 18 13:17:17 2011 | |
23 ------------------------------------------------------- |