SAS Datasets

In the lab we commonly use SAS as our main statistics package. There are times where you want to take a SAS dataset and do something with it in python. Typically you would have to use SAS to export the dataset as a CSV and then import it in python. However, there is a python module that allow you to directly access a SAS dataset and dump its contents into a pandas dataframe.

Install the sas7bdat library.

pip install sas7bdat --user

Once installed you can do the following.



In [1]:

    
import sas7bdat



In [5]:

    
with sas7bdat.SAS7BDAT('fbgn2coord.sas7bdat') as FH:
    df = FH.to_data_frame()









    



[fbgn2coord.sas7bdat] header length 65536 != 8192
[fbgn2coord.sas7bdat] [fbgn2coord.sas7bdat] header length 65536 != 8192
WARNING:/mnt/SHARE/McIntyre_Lab/useful_dmel_data/flybase557/sas_data/fbgn2coord.sas7bdat:[fbgn2coord.sas7bdat] [fbgn2coord.sas7bdat] header length 65536 != 8192



In [8]:

    
df.head()









    Out[8]:






  
    
      
      chrom
      end
      primary_fbgn
      start
      strand
    
  
  
    
      0
      3R
      2648518
      FBgn0000003
      2648220
      +
    
    
      1
      2R
      18060339
      FBgn0000008
      18024473
      +
    
    
      2
      3R
      12655771
      FBgn0000014
      12632936
      -
    
    
      3
      3R
      12797958
      FBgn0000015
      12752932
      -
    
    
      4
      3L
      16640982
      FBgn0000017
      16608966
      -

This package also comes with a nice command line tool that allows you to get the list of columns from a file.



In [9]:

    
%%bash
sas7bdat_to_csv --header fbgn2coord.sas7bdat









    









    



[fbgn2coord.sas7bdat] header length 65536 != 8192
[fbgn2coord.sas7bdat] Header:
	col_count_p1: 5
	col_count_p2: 0
	column_count: 5
	compression: None
	creator: None
	creator_proc: SORT
	date_created: 2014-12-04 18:04:03.851510
	date_modified: 2014-12-04 18:04:03.851510
	endianess: little
	file_type: DATA
	filename: fbgn2coord.sas7bdat
	header_length: 65536
	lcp: 4
	lcs: 0
	mix_page_row_count: 1123
	name: FBGN2COORD
	os_name: x86_64
	os_type: 3.13.0-40-generi
	page_count: 15
	page_length: 65536
	platform: unix
	row_count: 17294
	row_length: 56
	sas_release: 9.0401M0
	server_type: Linux
	u64: True

Contents of dataset "FBGN2COORD":
Num Name         Type   Length Format Label
--- ------------ ------ ------ ------ -----
  1 primary_fbgn string     11 $           
  2 chrom        string     25 $           
  3 start        number      8 BEST        
  4 end          number      8 BEST        
  5 strand       string      1 $



In [ ]:

	chrom	end	primary_fbgn	start	strand
0	3R	2648518	FBgn0000003	2648220	+
1	2R	18060339	FBgn0000008	18024473	+
2	3R	12655771	FBgn0000014	12632936	-
3	3R	12797958	FBgn0000015	12752932	-
4	3L	16640982	FBgn0000017	16608966	-