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annotate fml_gff_groomer/t/Feature_ID_mapping_W.txt @ 0:79726c328621 default tip

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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
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79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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2 GFFExamine started on Mon Apr 18 13:17:17 2011
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79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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5 ===Report on different level features from GFF file===
79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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7 FIRST level feature(s):
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8 ('Coding_transcript', 'gene')
79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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10 SECOND level feature(s):
79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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11 ('Coding_transcript', 'mRNA')
79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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13 THIRD level feature(s):
79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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14 ('Coding_transcript', 'CDS'), ('Coding_transcript', 'five_prime_UTR'), ('Coding_transcript', 'three_prime_UTR')
79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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16 GFF Parsing modules from publicly available packages like Bio-python, Bio-perl etc. are heavily dependent on feature identifier mapping.
79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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17 Here few features seems to be wrongly mapped to its child, which inturn cause problems while extracting the annotation based on feature identifier.
79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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19 Error in ID mapping: Level1 feature ('Coding_transcript', 'gene') maps to Level3 feature ('Coding_transcript', 'exon')
79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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20 Error in ID mapping: Level1 feature ('Coding_transcript', 'gene') maps to Level3 feature ('Coding_transcript', 'intron')
79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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22 GFFExamine finished at Mon Apr 18 13:17:17 2011
79726c328621 Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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23 -------------------------------------------------------