Update docs

sbslee · Sep 3, 2023 · bea3e00 · bea3e00
1 parent dda26c8
commit bea3e00
Show file tree

Hide file tree

Showing 2 changed files with 37 additions and 37 deletions.
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -7,7 +7,7 @@ Changelog
 * :issue:`67`: Fix bug in :meth:`pymaf.MafFrame.plot_waterfall` method where ``count=1`` was causing color mismatch.
 * Add new submodule ``pychip``.
 * Add new method :meth:`common.reverse_complement`.
-* Fix bug in :meth:`common.extract_sequence` where a long DNA sequence output was truncated.
+* Fix bug in :meth:`common.extract_sequence` method where a long DNA sequence output was truncated.
 * :issue:`68`: Refresh the variant consequences database from Ensembl VEP. The database's latest update was on May 31, 2021.
 
 0.36.0 (2022-08-12)

diff --git a/fuc/api/pymaf.py b/fuc/api/pymaf.py
@@ -103,42 +103,42 @@
 # additional information to find their correct Variant_Classification.
 
 VEP_CONSEQUENCES = {
- 'transcript_ablation': 'Splice_Site',
- 'splice_acceptor_variant': 'Splice_Site',
- 'splice_donor_variant': 'Splice_Site',
- 'stop_gained': 'Nonsense_Mutation',
- 'frameshift_variant': 'AMBIGUOUS',
- 'stop_lost': 'Nonstop_Mutation',
- 'start_lost': 'Translation_Start_Site',
- 'transcript_amplification': 'Intron',
- 'inframe_insertion': 'In_Frame_Ins',
- 'inframe_deletion': 'In_Frame_Del',
- 'missense_variant': 'Missense_Mutation',
- 'protein_altering_variant': 'AMBIGUOUS',
- 'splice_region_variant': 'Splice_Region',
- 'incomplete_terminal_codon_variant': 'Silent',
- 'start_retained_variant': 'Silent',
- 'stop_retained_variant': 'Silent',
- 'synonymous_variant': 'Silent',
- 'coding_sequence_variant': 'Missense_Mutation',
- 'mature_miRNA_variant': 'RNA',
- '5_prime_UTR_variant': "5'UTR",
- '3_prime_UTR_variant': "3'UTR",
- 'non_coding_transcript_exon_variant': 'RNA',
- 'intron_variant': 'Intron',
- 'NMD_transcript_variant': 'Silent',
- 'non_coding_transcript_variant': 'RNA',
- 'upstream_gene_variant': "5'Flank",
- 'downstream_gene_variant': "3'Flank",
- 'TFBS_ablation': 'Targeted_Region',
- 'TFBS_amplification': 'Targeted_Region',
- 'TF_binding_site_variant': 'IGR',
- 'regulatory_region_ablation': 'Targeted_Region',
- 'regulatory_region_amplification': 'Targeted_Region',
- 'feature_elongation': 'Targeted_Region',
- 'regulatory_region_variant': 'IGR',
- 'feature_truncation': 'Targeted_Region',
- 'intergenic_variant': 'IGR',
+ 'transcript_ablation':  'Splice_Site',
+ 'splice_acceptor_variant':  'Splice_Site',
+ 'splice_donor_variant':  'Splice_Site',
+ 'stop_gained':  'Nonsense_Mutation',
+ 'frameshift_variant':  'AMBIGUOUS',
+ 'stop_lost':  'Nonstop_Mutation',
+ 'start_lost':  'Translation_Start_Site',
+ 'transcript_amplification':  'Intron',
+ 'inframe_insertion':  'In_Frame_Ins',
+ 'inframe_deletion':  'In_Frame_Del',
+ 'missense_variant':  'Missense_Mutation',
+ 'protein_altering_variant':  'AMBIGUOUS',
+ 'splice_region_variant':  'Splice_Region',
+ 'incomplete_terminal_codon_variant':  'Silent',
+ 'start_retained_variant':  'Silent',
+ 'stop_retained_variant':  'Silent',
+ 'synonymous_variant':  'Silent',
+ 'coding_sequence_variant':  'Missense_Mutation',
+ 'mature_miRNA_variant':  'RNA',
+ '5_prime_UTR_variant':  "5'UTR",
+ '3_prime_UTR_variant':  "3'UTR",
+ 'non_coding_transcript_exon_variant':  'RNA',
+ 'intron_variant':  'Intron',
+ 'NMD_transcript_variant':  'Silent',
+ 'non_coding_transcript_variant':  'RNA',
+ 'upstream_gene_variant':  "5'Flank",
+ 'downstream_gene_variant':  "3'Flank",
+ 'TFBS_ablation':  'Targeted_Region',
+ 'TFBS_amplification':  'Targeted_Region',
+ 'TF_binding_site_variant':  'IGR',
+ 'regulatory_region_ablation':  'Targeted_Region',
+ 'regulatory_region_amplification':  'Targeted_Region',
+ 'feature_elongation':  'Targeted_Region',
+ 'regulatory_region_variant':  'IGR',
+ 'feature_truncation':  'Targeted_Region',
+ 'intergenic_variant':  'IGR',
  'splice_donor_5th_base_variant': 'AMBIGUOUS',
  'splice_donor_region_variant': 'AMBIGUOUS',
  'splice_polypyrimidine_tract_variant': 'AMBIGUOUS',