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<!-- saved from url=(0093)http://www.bioinformatics.org/jobs/index.php?group_id=101&show=archives&offset=1680&length=24 --> | |
<html style="zoom: 100%; "><style>#bitly_expanded_container { | |
position:absolute; | |
/* round the corners */ | |
bottom:1px; | |
z-index:5000; | |
/* width:100%;*/ | |
left:0px; | |
display:none; |
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#!/usr/bin/perl | |
# Author : Kamil Slowikowski <kslowikowski@gmail.com> | |
# Date : March 23, 2011 | |
# Version : 0.1 | |
# Description : Modified code from | |
# http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook | |
use strict; | |
use warnings; |
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#!/usr/bin/env python | |
"""merge_intervals.py | |
Merge tab-delimited intervals: | |
cat tissue1.txt | |
chr1,1-2 | |
chr1,3-4 | |
chr1,5-6 |
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#!/usr/bin/env python | |
"""ncbi_fetch.py | |
Query NCBI and fetch the results into gzipped files. Files will be saved in | |
the current directory as: 001-050.gz, 051-100.gz, etc. | |
You can then do: | |
zcat 001-050.gz | head |
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""" | |
genomic_intervals.py | |
Kamil Slowikowski | |
February 27, 2014 | |
Genomic intervals: 0-based, 1-based, overlaps, and distance | |
=========================================================== | |
This document describes genomic intervals and includes source code for testing | |
overlap and calculating distance between intervals. |
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""" | |
VCF.py | |
Kamil Slowikowski | |
October 30, 2013 | |
Read VCF files. Works with gzip compressed files and pandas. | |
Note: This module ignores the genotype columns because | |
I didn't need them at the time of writing. |
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""" | |
chromtree.py | |
Kamil Slowikowski | |
October 30, 2013 | |
This module is a simple extension of | |
bx.intervals.intersection.IntervalTree | |
to neatly handle a dictionary of interval trees. |
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#!/usr/bin/env python | |
""" | |
GTF.py | |
Kamil Slowikowski | |
December 24, 2013 | |
Read GFF/GTF files. Works with gzip compressed files and pandas. | |
http://useast.ensembl.org/info/website/upload/gff.html |
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