mpschr

[DEBUG] Version 2.8
[DEBUG] Connecting to new host www.google.com
Please initiate a query.
googler (? for help) acute myeloid leukemia
[DEBUG] Fetching URL /search?ie=UTF-8&num=10&oe=UTF-8&q=acute+myeloid+leukemia&start=0
[DEBUG] Redirecting to URL https://ipv6.google.com/sorry/index?continue=https://www.google.com/search%3Fie%3DUTF-8%26num%3D10%26oe%3DUTF-8%26q%3Dacute%2Bmyeloid%2Bleukemia%26start%3D0&q=CGMSECoCgQmaQAB4QMRd6gMP4vQY_OLfvwUiGQDxp4NLo2ZqN-VW7TGV-fqAOK9YF7Dl4DU
[DEBUG] Connecting to new host ipv6.google.com
[DEBUG] Fetching URL /sorry/index?continue=https://www.google.com/search%3Fie%3DUTF-8%26num%3D10%26oe%3DUTF-8%26q%3Dacute%2Bmyeloid%2Bleukemia%26start%3D0&q=CGMSECoCgQmaQAB4QMRd6gMP4vQY_OLfvwUiGQDxp4NLo2ZqN-VW7TGV-fqAOK9YF7Dl4DU
Traceback (most recent call last):
  File "/usr/local/bin/googler", line 2166, in <module>

mpschr

[2015-06-26T08:57Z] Timing: organize samples
[2015-06-26T08:57Z] multiprocessing: organize_samples
[2015-06-26T08:57Z] Using input YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml
[2015-06-26T08:57Z] Checking sample YAML configuration: /home/michael/Documents/projects/exon/config/extest.yaml
[2015-06-26T08:57Z] Testing minimum versions of installed programs
[2015-06-26T08:57Z] Timing: alignment preparation
[2015-06-26T08:57Z] multiprocessing: prep_align_inputs
[2015-06-26T09:55Z] multiprocessing: disambiguate_split
[2015-06-26T09:55Z] Timing: alignment
[2015-06-26T09:55Z] multiprocessing: process_alignment

mpschr

2015-06-11 14:53:37 +0200

export FTP_PASSIVE=1 && /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/INSTALL.pl -a a -d /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib -c /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/share/data

Using non-default installation directory /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib - you will probably need to add /home/mpschr/bin/bcbionextgen/tools/Cellar/vep/79_2015-04-13/lib to your PERL5LIB

Setting up directories

Downloading required files
 - fetching ensembl

mpschr

d3.svg.legend provides for a simple legend that can be displayed horizontally or vertically and accepts a few different d3 scale types.

mpschr

import pandas
import logging

def multi_df_join(df_dict):
    """
    Takes a list of dataframes with the same primary key (id) and merges the columns, using
    the dictionary keys as suffixes in case there are conflicts with the column names.

    :param df_dict: A dictionary where keys are strings (collision suffixes) and values are DataFrames
    :return pandas.DataFrame: The merged data frames

mpschr

mpschr

__author__ = "Yasunobu OKAMURA, Michael P SCHROEDER"
__copyright__ = "Copyright (c) 2012 Y.Okamura"
__license__ = "GPL v3+"

import xml.parsers.expat
import networkx as nx

class XGMMLParserHelper(object):
    """
    Creates an instance of the XGMML parser that allows to import the

mpschr

## Create a script that deletes all the local and remote tags you want. Do
## not hasten through the process


## 1.
## What tags do you want to delete? substitute YOURPATTERN with the pattern you want to match against
git tag -l | awk '/.*YOURPATTERN.*$/ {print "git tag -d "$1"\ngit push origin :refs/tags/"$1}' > delete-tags.sh

## 2.
## Check the delete-tags.sh to see if everything is ok.