CODEWITHSUNDEEP
pythonlistreadfilesplicedna-sequence
PaulBarr
PaulBarr

Reputation: 949

Read a text file into python by splitting the file into list items according to a set of characters

I have a plain text file with the following contents:

@M00964: XXXXX
YYY
+
ZZZZ 
@M00964: XXXXX
YYY
+
ZZZZ
@M00964: XXXXX
YYY
+
ZZZZ

and I would like to read this into a list split into items according to the ID code @M00964, i.e. :

['@M00964: XXXXX
YYY
+
ZZZZ' 
'@M00964: XXXXX
YYY
+
ZZZZ'
'@M00964: XXXXX
YYY
+
ZZZZ']

I have tried using 

in_file = open(fileName,"r")
sequences = in_file.read().split('@M00964')[1:]
in_file.close()

but this removes the ID sequence @M00964. Is there any way to keep this ID sequence in?

As an additional question is there any way of maintaining white space in a list (rather than have /n symbols).

My overall aim is to read in this set of items, take the first 2, for example, and write them back to a text file maintaining all of the original formatting.

Upvotes: 3

Views: 2729

Answers (3)

sshashank124
sshashank124

Reputation: 32189

Specific to your example, can't you just do something as follows:

in_file = open(fileName, 'r')
file = in_file.readlines()

new_list = [''.join(file[i*4:(i+1)*4]) for i in range(int(len(file)/4))]
list_no_n = [item.replace('\n','') for item in new_list]

print new_list
print list_no_n

[EXPANDED FORM]

new_list = []
for i in range(int(len(file)/4)): #Iterates through 1/4 of the length of the file lines.
                                  #This is because we will be dealing in groups of 4 lines
    new_list.append(''.join(file[i*4:(i+1)*4])) #Joins four lines together into a string and adds it to the new_list

[Writing to new file]

write_list = ''.join(new_list).split('\n')
output_file = open(filename, 'w')
output_file.writelines(write_list)

Upvotes: 0

Simon
Simon

Reputation: 2960

Just split on the @ sign instead:

with open(fileName,"r") as in_file:
    sequences = in_file.read().replace("@","###@").split('###')

Upvotes: 0

Steven Rumbalski
Steven Rumbalski

Reputation: 45542

If your file is large and you don't want hold the whole thing in memory you can just iterate over individual records using this helper function:

def chunk_records(filepath)
    with open(filepath, 'r') as f:
        record = []
        for line in f:
            # could use regex for more complicated matching
            if line.startswith('@M00964') and record:
                yield ''.join(record)
                record = []
            else:
                record.append(line)
        if record:
            yield ''.join(record)

Use it like

for record in chunk_records('/your/filename.txt'):
    ...

Or if you want the whole thing in memory:

records = list(chunk_records('/your/filename.txt'))

Upvotes: 3

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