jorvis

#!/usr/bin/env python3

import sys
from collections import defaultdict

infile = sys.argv[1]

sums = defaultdict(int)

for line in open(infile):

jorvis

# GEO DATA FROM GSExxxx ID
----------------------------
^SERIES = GSE65633
!Series_title = RNA-seq analysis of neonatal mouse cochlear hair cells
!Series_geo_accession = GSE65633
!Series_pubmed_id = 25855195
!Series_summary = This study examined transcripts that are enriched in neonatal mouse cochlear hair cells. Hair cells were purified by FACS sorting for GFP fluorescence from the cochleas of transgenic mice in which the endogenous Atoh1 gene was fused with GFP
!Series_overall_design = Two replicates of GFP+ hair cells were compared with all other cochlear cell types that were GFP-
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Andrew,K,Groves

jorvis

sc.pl.violin(adata, gene.gene_symbol, group_by='mygroups', save="{0}.png".format(pid), linewidth=0.3)

Yields:
Traceback (most recent call last):
  File "/var/www/gear/cgi/get_violin_plot.cgi", line 81, in <module>
    main()
  File "/var/www/gear/cgi/get_violin_plot.cgi", line 68, in main
    sc.pl.violin(adata, gene.gene_symbol, group_by='mygroups', save="{0}.png".format(pid), linewidth=0.3)
TypeError: violin() got an unexpected keyword argument 'linewidth'

jorvis

(custom-set-variables
  ;; custom-set-variables was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.
  ;; Your init file should contain only one such instance.
  ;; If there is more than one, they won't work right.
 '(inhibit-startup-screen t))
(custom-set-faces
  ;; custom-set-faces was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.
  ;; Your init file should contain only one such instance.

jorvis

SELECT f.feature_id
  FROM feature f
       JOIN cvterm ON f.type_id=cvterm.cvterm_id
 WHERE cvterm.name = 'polypeptide'
   AND f.feature_id NOT IN (
        SELECT f.feature_id
          FROM feature f
               JOIN cvterm ON f.type_id=cvterm.cvterm_id
               JOIN featureprop fp ON f.feature_id=fp.feature_id
               JOIN cvterm gpn ON fp.type_id=gpn.cvterm_id

jorvis

.
├── bin
│   ├── add_gff3_locus_tags.py
│   ├── append_to_column_9_value.py
... lots of files ...
│   ├── validate_feature_boundaries_on_molecules.py
│   └── write_fasta_from_gff.py
├── biocode
│   ├── annotation.py
│   ├── data

jorvis

include README.rst
graft data
include LICENSE

jorvis

#!/usr/bin/env python3

"""
Kids do great playing Minecraft together but fight when deciding
in whose world to play? What mode?  Difficulty level?

I give them 1 minute to work it out before I run this script
and let it pick instead.
"""

jorvis

#!/usr/bin/env python3

"""
This assumes you're using either Gnome3 or Unity and have a directory of wallpapers
here:

~/Pictures/Wallpaper

You probably want to set this as a cron to execute at a certain interval: