In [119]:

    

import pandas as pd


    

In [120]:

    

df = pd.read_table("../data/refseqOutVarSeq", dtype = {'start': int, 'stop': int}, usecols= [0,1,2,3,7])


    

    




/home/glen/miniconda3/lib/python3.5/site-packages/IPython/core/interactiveshell.py:2717: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False.
  interactivity=interactivity, compiler=compiler, result=result)

In [121]:

    

df.head()


    

    
Out[121]:







  

    

      

      
Chromosome
      
Start
      
Stop
      
Gene Name
      
Strand
    
  
  

    

      
0
      
1
      
11873
      
14409
      
DDX11L1
      
+
    
    

      
1
      
1
      
14361
      
29370
      
WASH7P
      
-
    
    

      
2
      
1
      
17368
      
17436
      
MIR6859-1
      
-
    
    

      
3
      
1
      
30365
      
30503
      
MIR1302-2
      
+
    
    

      
4
      
1
      
34610
      
36081
      
FAM138A
      
-
    
  

In [122]:

    

dfgenes = pd.read_excel("../data/GeneKB01.xlsx")


    

In [123]:

    

myeloidList = list(dfgenes['GeneSymbol'])


    

In [124]:

    

df = df[df['Gene Name'].isin(myeloidList)]
bygene = df.groupby('Gene Name')
bygene.nunique()


    

    
Out[124]:







  

    

      

      
Chromosome
      
Start
      
Stop
      
Gene Name
      
Strand
    
    

      
Gene Name
      

      

      

      

      

    
  
  

    

      
ABL1
      
1
      
2
      
1
      
1
      
1
    
    

      
AKT1
      
1
      
1
      
2
      
1
      
1
    
    

      
ALK
      
1
      
1
      
1
      
1
      
1
    
    

      
APC
      
1
      
2
      
1
      
1
      
1
    
    

      
ASXL1
      
1
      
1
      
2
      
1
      
1
    
    

      
ATM
      
1
      
1
      
1
      
1
      
1
    
    

      
BCOR
      
1
      
1
      
2
      
1
      
1
    
    

      
BCORL1
      
1
      
1
      
1
      
1
      
1
    
    

      
BRAF
      
1
      
1
      
1
      
1
      
1
    
    

      
CALR
      
1
      
1
      
1
      
1
      
1
    
    

      
CBL
      
1
      
1
      
1
      
1
      
1
    
    

      
CBLB
      
1
      
1
      
5
      
1
      
1
    
    

      
CDH1
      
1
      
1
      
1
      
1
      
1
    
    

      
CDKN2A
      
1
      
1
      
3
      
1
      
1
    
    

      
CEBPA
      
1
      
1
      
1
      
1
      
1
    
    

      
CSF1R
      
1
      
1
      
2
      
1
      
1
    
    

      
CSF3R
      
1
      
1
      
1
      
1
      
1
    
    

      
CTNNB1
      
1
      
2
      
2
      
1
      
1
    
    

      
DNMT3A
      
1
      
2
      
4
      
1
      
1
    
    

      
EGFR
      
1
      
3
      
5
      
1
      
1
    
    

      
ERBB2
      
1
      
2
      
2
      
1
      
1
    
    

      
ERBB4
      
1
      
1
      
1
      
1
      
1
    
    

      
ETV6
      
1
      
1
      
1
      
1
      
1
    
    

      
EZH2
      
1
      
1
      
2
      
1
      
1
    
    

      
FBXW7
      
1
      
2
      
4
      
1
      
1
    
    

      
FGFR1
      
1
      
1
      
2
      
1
      
1
    
    

      
FGFR2
      
1
      
2
      
5
      
1
      
1
    
    

      
FGFR3
      
1
      
1
      
1
      
1
      
1
    
    

      
FLT3
      
1
      
1
      
1
      
1
      
1
    
    

      
GATA1
      
1
      
1
      
1
      
1
      
1
    
    

      
...
      
...
      
...
      
...
      
...
      
...
    
    

      
NOTCH1
      
1
      
1
      
1
      
1
      
1
    
    

      
NPM1
      
1
      
1
      
2
      
1
      
1
    
    

      
NRAS
      
1
      
1
      
1
      
1
      
1
    
    

      
PDGFRA
      
1
      
3
      
2
      
1
      
1
    
    

      
PHF6
      
1
      
1
      
2
      
1
      
1
    
    

      
PIK3CA
      
1
      
1
      
1
      
1
      
1
    
    

      
PML
      
1
      
1
      
3
      
1
      
1
    
    

      
PTEN
      
1
      
1
      
1
      
1
      
1
    
    

      
PTPN11
      
1
      
1
      
2
      
1
      
1
    
    

      
RAD21
      
1
      
1
      
1
      
1
      
1
    
    

      
RB1
      
1
      
1
      
1
      
1
      
1
    
    

      
RET
      
1
      
1
      
2
      
1
      
1
    
    

      
RUNX1
      
1
      
2
      
2
      
1
      
1
    
    

      
SETBP1
      
1
      
2
      
2
      
1
      
1
    
    

      
SF3B1
      
1
      
2
      
1
      
1
      
1
    
    

      
SMAD4
      
1
      
1
      
1
      
1
      
1
    
    

      
SMARCB1
      
1
      
1
      
1
      
1
      
1
    
    

      
SMC1A
      
1
      
1
      
1
      
1
      
1
    
    

      
SMC3
      
1
      
1
      
1
      
1
      
1
    
    

      
SMO
      
1
      
1
      
1
      
1
      
1
    
    

      
SRC
      
1
      
2
      
1
      
1
      
1
    
    

      
SRSF2
      
1
      
1
      
1
      
1
      
1
    
    

      
STAG2
      
1
      
3
      
1
      
1
      
1
    
    

      
STK11
      
1
      
1
      
1
      
1
      
1
    
    

      
TET2
      
1
      
2
      
2
      
1
      
1
    
    

      
TP53
      
1
      
1
      
2
      
1
      
1
    
    

      
U2AF1
      
1
      
1
      
1
      
1
      
1
    
    

      
VHL
      
1
      
1
      
1
      
1
      
1
    
    

      
WT1
      
1
      
1
      
2
      
1
      
1
    
    

      
ZRSR2
      
1
      
1
      
1
      
1
      
1
    
  

81 rows × 5 columns

In [125]:

    

df[df['Gene Name'] == 'DNMT3A']


    

    
Out[125]:







  

    

      

      
Chromosome
      
Start
      
Stop
      
Gene Name
      
Strand
    
  
  

    

      
6845
      
2
      
25455829
      
25475000
      
DNMT3A
      
-
    
    

      
6846
      
2
      
25455829
      
25475184
      
DNMT3A
      
-
    
    

      
6847
      
2
      
25455829
      
25564784
      
DNMT3A
      
-
    
    

      
6848
      
2
      
25455829
      
25565459
      
DNMT3A
      
-
    
    

      
6849
      
2
      
25504320
      
25564784
      
DNMT3A
      
-
    
    

      
6850
      
2
      
25504320
      
25565459
      
DNMT3A
      
-
    
  

In [126]:

    

bygene.apply()


    

    




---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-126-e8e9da76f2c8> in <module>()
----> 1 bygene.apply()

TypeError: apply() missing 1 required positional argument: 'func'

In [127]:

    

def minmax(group):
    mychr = 'chr' + str(group['Chromosome'].iloc[0])
    mymax = pd.np.max([pd.np.max(group['Start']),pd.np.max(group['Stop'])])
    mymin = pd.np.min([pd.np.min(group['Start']),pd.np.min(group['Stop'])])
    return pd.Series({'chr': mychr, 'start': mymin, 'stop': mymax})


    

In [128]:

    

tempdf = bygene.apply(minmax)


    

In [129]:

    

tempdf.to_csv("refseq_start_stop.tsv", sep="\t")


    

In [ ]:

    




    

In [ ]: