new variant class and plots

.gitignore

@@ -26,6 +26,7 @@ dask-worker-space/
 *.err
 *.out
 .DS_Store
+*chr.csv
 
 # PyInstaller
 #  Usually these files are written by a python script from a template

configs/var_class.yaml

@@ -1,6 +1,6 @@
- NMD_transcript_variant,synonymous_variant: NMD
+ NMD_transcript_variant,synonymous_variant: synonymous
  synonymous_variant: synonymous
- 2kb_downstream_variant,NMD_transcript_variant: NMD
+ 2kb_downstream_variant,NMD_transcript_variant: intergenic
  frameshift_elongation: frameshift elongation
  processed_transcript: other RNA
  stop_gained: stop gained
@@ -10,7 +10,7 @@
  intron_variant,processed_transcript: intron
  missense_variant: missense
  frameshift_truncation: frameshift truncation
- NMD_transcript_variant,3_prime_UTR_variant: NMD
+ NMD_transcript_variant,3_prime_UTR_variant: 3 prime UTR
  3_prime_UTR_variant: 3 prime UTR
  5_prime_UTR_variant: 5 prime UTR
  2kb_downstream_variant,processed_transcript: other RNA
@@ -19,87 +19,87 @@
  2kb_upstream_variant,lnc_RNA: other RNA
  2kb_upstream_variant: intergenic
  2kb_upstream_variant,processed_transcript: other RNA
- intron_variant,NMD_transcript_variant: NMD
+ intron_variant,NMD_transcript_variant: intron
  lnc_RNA: other RNA
- NMD_transcript_variant,stop_gained: NMD
- missense_variant,NMD_transcript_variant: NMD
- 2kb_downstream_variant,NSD_transcript: NMD
+ NMD_transcript_variant,stop_gained: stop gained
+ missense_variant,NMD_transcript_variant: missense
+ 2kb_downstream_variant,NSD_transcript: intergenic
  2kb_downstream_variant: intergenic
  complex_substitution,missense_variant: missense
  complex_substitution,frameshift_truncation: frameshift truncation
- complex_substitution,frameshift_truncation,NMD_transcript_variant: NMD
- intron_variant,NMD_transcript_variant,splice_site_variant: NMD
- 2kb_upstream_variant,NMD_transcript_variant: NMD
+ complex_substitution,frameshift_truncation,NMD_transcript_variant: frameshift truncation
+ intron_variant,NMD_transcript_variant,splice_site_variant: splice site
+ 2kb_upstream_variant,NMD_transcript_variant: intergenic
  2kb_upstream_variant,misc_RNA: other RNA
  complex_substitution,frameshift_elongation,intron_variant: frameshift elongation
  2kb_downstream_variant,misc_RNA: other RNA
  missense_variant,start_lost: start lost
- NSD_transcript: NMD
- NMD_transcript_variant,5_prime_UTR_variant: NMD
+ NSD_transcript: other
+ NMD_transcript_variant,5_prime_UTR_variant: 5 prime UTR
  splice_site_variant: splice site
  stop_retained_variant: stop retained
  2kb_upstream_variant,miRNA: other RNA
  inframe_insertion: inframe insertion
- frameshift_truncation,NMD_transcript_variant: NMD
- frameshift_elongation,NMD_transcript_variant: NMD
+ frameshift_truncation,NMD_transcript_variant: frameshift truncation
+ frameshift_elongation,NMD_transcript_variant: frameshift elongation
  frameshift_truncation,stop_gained: frameshift truncation
  inframe_deletion: inframe deletion
  2kb_downstream_variant,snRNA: other RNA
- 2kb_upstream_variant,NSD_transcript: NMD
- inframe_deletion,NMD_transcript_variant: NMD
- frameshift_truncation,NMD_transcript_variant,stop_gained: NMD
- missense_variant,start_lost,NMD_transcript_variant: NMD
+ 2kb_upstream_variant,NSD_transcript: intergenic
+ inframe_deletion,NMD_transcript_variant: inframe deletion
+ frameshift_truncation,NMD_transcript_variant,stop_gained: frameshift truncation
+ missense_variant,start_lost,NMD_transcript_variant: start lost
  2kb_upstream_variant,snRNA: other RNA
- intron_variant,NSD_transcript: NMD
+ intron_variant,NSD_transcript: intron
  frameshift_elongation,stop_gained: frameshift elongation
- NMD_transcript_variant,splice_site_variant: NMD
+ NMD_transcript_variant,splice_site_variant: splice site
  frameshift_truncation,stop_lost: frameshift truncation
  2kb_downstream_variant,snoRNA: other RNA
  inframe_insertion,stop_gained: stop gained
  ribozyme: other RNA
- NSD_transcript,5_prime_UTR_variant: NMD
+ NSD_transcript,5_prime_UTR_variant: 5 prime UTR
  complex_substitution,frameshift_elongation: frameshift elongation
  polymorphic_pseudogene,5_prime_UTR_variant: other RNA
  polymorphic_pseudogene: other RNA
- NMD_transcript_variant: NMD
+ NMD_transcript_variant: other
  frameshift_truncation,stop_lost,stop_retained_variant,3_prime_UTR_variant: frameshift truncation
  2kb_downstream_variant,stop_lost: stop lost
  complex_substitution,inframe_deletion: inframe deletion
  complex_substitution: complex substitution
- NMD_transcript_variant,stop_lost: NMD
- inframe_insertion,NMD_transcript_variant: NMD
+ NMD_transcript_variant,stop_lost: stop lost
+ inframe_insertion,NMD_transcript_variant: inframe insertion
  2kb_upstream_variant,ribozyme: other RNA
- frameshift_elongation,NMD_transcript_variant,stop_gained: NMD
+ frameshift_elongation,NMD_transcript_variant,stop_gained: frameshift elongation
  complex_substitution,stop_gained: stop gained
  exon_loss_variant,frameshift_truncation: frameshift truncation
  2kb_downstream_variant,stop_lost,3_prime_UTR_variant: stop lost
  inframe_deletion,stop_gained: stop gained
  polymorphic_pseudogene,3_prime_UTR_variant: other RNA
- complex_substitution,missense_variant,NMD_transcript_variant: NMD
+ complex_substitution,missense_variant,NMD_transcript_variant: missense
  snRNA: other RNA
  2kb_upstream_variant,snoRNA: other RNA
- exon_loss_variant,frameshift_truncation,NMD_transcript_variant: NMD
+ exon_loss_variant,frameshift_truncation,NMD_transcript_variant: frameshift truncation
  miRNA: other RNA
  complex_substitution,inframe_insertion,intron_variant: complex substitution
  stop_lost: stop lost
- complex_substitution,frameshift_elongation,NMD_transcript_variant: NMD
+ complex_substitution,frameshift_elongation,NMD_transcript_variant: frameshift elongation
  exon_loss_variant,inframe_deletion: exon loss variant
  frameshift_truncation,start_lost: frameshift truncation
  complex_substitution,inframe_insertion,stop_gained: stop gained
  misc_RNA: other RNA
- NMD_transcript_variant,stop_retained_variant: NMD
+ NMD_transcript_variant,stop_retained_variant: stop retained
  start_lost,5_prime_UTR_variant: start lost
  complex_substitution,inframe_insertion,intron_variant,missense_variant: complex substitution
- complex_substitution,frameshift_elongation,intron_variant,NMD_transcript_variant: NMD
- complex_substitution,inframe_insertion,intron_variant,NMD_transcript_variant: NMD
+ complex_substitution,frameshift_elongation,intron_variant,NMD_transcript_variant: frameshift elongation
+ complex_substitution,inframe_insertion,intron_variant,NMD_transcript_variant: complex substitution
  intron_variant,polymorphic_pseudogene: other RNA
  2kb_downstream_variant,intron_variant,stop_lost,3_prime_UTR_variant: stop lost
  complex_substitution,inframe_insertion: complex substitution
  start_retained_variant: start retained
  2kb_upstream_variant,rRNA: other RNA
  complex_substitution,inframe_deletion,missense_variant: complex substitution
  snoRNA: other RNA
- inframe_insertion,NMD_transcript_variant,stop_gained: NMD
+ inframe_insertion,NMD_transcript_variant,stop_gained: stop gained
  complex_substitution,synonymous_variant: complex substitution
- NMD_transcript_variant,stop_lost,3_prime_UTR_variant: NMD
+ NMD_transcript_variant,stop_lost,3_prime_UTR_variant: stop lost
  frameshift_elongation,stop_lost: frameshift elongation