python - Remove rows in which string contains other letters than A,C,T,G,N

Question

I'm fairly new to numpy and pandas, let's say that I have a 2D numpy array and I need to delete all rows in which the second value contain only the letters 'A', 'C', 'T', 'G' and 'N'

file = 
[['id' 'genome'],
 ['0' 'ATGTTTGTTTTT'],
 ['1' 'ATGTTTGTXXXX'],
 ['2' 'ATGDD2GTTTTT']
]

so after filtering I can get this

[['id' 'genome'],
 ['0' 'ATGTTTGTTTTT']]

I wanted to do 3 for loops that are checking each char one by one but this is sooo slow when I have 500 rows

question from:https://stackoverflow.com/questions/66047320/remove-rows-in-which-string-contains-other-letters-than-a-c-t-g-n

Answer 1

Use Series.str.contains with values and ^ for start and $ for end of string:

file = [['id', 'genome'],
 ['0', 'ATGTTTGTTTTT'],
 ['1', 'ATGTTTGTXXXX'],
 ['2', 'ATGDD2GTTTTT']
]
 
df = pd.DataFrame(file[1:], columns=file[0])
print (df)


df = df[df['genome'].str.contains('^[ACTGN]+$')]
print (df)
  id        genome
0  0  ATGTTTGTTTTT