Alistair Walsh alistairwalsh

## pubmed_search.py
"""Tools for searching Pubmed for a list of PMIDs.

The goal here is to search for many PMIDs at once, since searching
sequentially can take a long time. Using the the BioPython Entrez module
is super convenient to this end.

The results results are returned in a simple dictionary format.
"""


## plos_sunburnt_demo.py
#Sample PLOS api code for use with python Solr library Sunburnt
#( https://github.com/tow/sunburnt )
#!Note! requires sunburnt's external libraries: httplib2,lxml
#https://groups.google.com/d/topic/plos-api-developers/zv591sFz6TM/discussion

import sunburnt,urllib2
class PlosInterface(sunburnt.SolrInterface):
    def __init__(self,api_key):
        plos_url = "http://api.plos.org/search"
        #either

## input_other.csv

          
            1
            2.12371
            0

            
              2
              1.05275
              0

            
              3
              0.865794
              0

            
              4
              0.933986
              0

            
              5
              1.09092
              0

            
              6
              1.22333
              0

            
              7
              1.54639
              0

            
              8
              1.24223
              0

            
              9
              1.10928
              0

            
              10
              1.16232
              0

## imputant.py
import numpy as np
from sklearn.preprocessing import Imputer

#generate some data
df1 = np.array(np.random.randn(1000)).reshape(100,10)

#make some values 'NaN'
df1[(df1>-.05) & (df1<.05)] = np.nan

X = df1

## function and loop
def peel(name):
  return name[1:-1]

bag = ['dutch cream','desiree','kifler']

for potato in bag:
  print peel(potato)
	"""Tools for searching Pubmed for a list of PMIDs.

	The goal here is to search for many PMIDs at once, since searching
	sequentially can take a long time. Using the the BioPython Entrez module
	is super convenient to this end.

	The results results are returned in a simple dictionary format.
	"""
	#Sample PLOS api code for use with python Solr library Sunburnt
	#( https://github.com/tow/sunburnt )
	#!Note! requires sunburnt's external libraries: httplib2,lxml
	#https://groups.google.com/d/topic/plos-api-developers/zv591sFz6TM/discussion

	import sunburnt,urllib2
	class PlosInterface(sunburnt.SolrInterface):
	def __init__(self,api_key):
	plos_url = "http://api.plos.org/search"
	#either
	1	2.12371	0
	2	1.05275	0
	3	0.865794	0
	4	0.933986	0
	5	1.09092	0
	6	1.22333	0
	7	1.54639	0
	8	1.24223	0
	9	1.10928	0
	10	1.16232	0
	import numpy as np
	from sklearn.preprocessing import Imputer

	#generate some data
	df1 = np.array(np.random.randn(1000)).reshape(100,10)

	#make some values 'NaN'
	df1[(df1>-.05) & (df1<.05)] = np.nan

	X = df1
	def peel(name):
	return name[1:-1]

	bag = ['dutch cream','desiree','kifler']

	for potato in bag:
	print peel(potato)