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@dangunter
dangunter / pbar.py
Created May 8, 2016 15:33
Simple Python text progress bar
"""
Text progress bar
"""
import sys
class PBar(object):
"""Text progress bar.
"""
c0 = '.' # left end marker
c1 = '_' # completed char
@dangunter
dangunter / Interval-tree-example.ipynb
Created December 11, 2015 16:07
Example of using Python “intervaltree” module to find intervals overlapping some input interval
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@dangunter
dangunter / wbnotes-data-1apr2015
Last active August 29, 2015 14:18
data redesign discussion notes 4/1/2015
# Weaknesses
* Sharing/granularity
* Versioning
* Narratives together with bio objs
* References
- shock vs. W.S. vs. CDS
- permissions relaxed on refs
- all refs hierarchical/one-way
- data copies may not be complete
@dangunter
dangunter / crd-skills
Last active August 29, 2015 14:18
CRD skills list
AJAX
AMR
AngularJS
Apache HTTPD
Assembly
BLAST - Basic Local Alignment Search Tool
C/C++
CGI
cloud computing
CSS
@dangunter
dangunter / Mapping.ipynb
Created January 24, 2015 03:34
SEED mapping example
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#!/usr/bin/env python
"""
Generate many fireworks workflows.
"""
import argparse
import os
import sys
def main():
p = argparse.ArgumentParser(description="Generate fireworks")
@dangunter
dangunter / mg-run-history
Last active December 15, 2015 03:28
Generate run history from materials project database
## Generate graph of run history
Generating the graph requires 2 scripts
1) A Python script to extract the dates of each compound from the
database. Replace DB, USER and PASSWORD below with appropriate values:
./mg_run_history.py DB USER PASSWORD --port 27018 > runs.csv
@dangunter
dangunter / dump_blipp_as_csv.py
Created April 6, 2012 21:35
Dump from Mongo database of (old-style) Blipp Periscope data to CSV
"""
Given x,y,z MIDs, dump the data values in range a to b to a CSV
"""
import argparse
import os
import sys
#
import pymongo
from pymongo_mr import base as mr_base