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#!/usr/bin/env python3 | |
import sys | |
from collections import defaultdict | |
infile = sys.argv[1] | |
sums = defaultdict(int) | |
for line in open(infile): |
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# 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 |
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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' |
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(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. |
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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 |
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. | |
├── 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 |
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include README.rst | |
graft data | |
include LICENSE |
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#!/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. | |
""" |
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#!/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: |