how to retrieve string from a large file

Question

I have written a code in which "IDS.txt" is a tab deliminated text file contains ID in the manner given below in which first column represent ID second starting index and third column ending index.

IDs.txt-------

"complete.txt"

the script which i have write given bellow to retrieve the string fragment according to "IDs.txt" it's NOT working please help what changes should i make to correct the code

with open("\Users\Zebrafish\Desktop\IDs.txt") as f: # will get input from the text
    for line in f:
        c = line.split("\t")                  
        for i, x in enumerate(c):                #passing values to  start and end variables 
            if i == 1:
               start = x
            elif i == 2:
                end =  x
            elif i == 0:
                 gene_name = x
        infile = open("/Users/Zebrafish/Desktop/complete.txt")  #file to get large string data 
        for seq in infile:
            seqnew = seq.split("\t")                       # get data as single line 
        retrived = seqnew[int(start):int(end)]             #retrieve  fragment 
        print retrived

Answer 1

I don't know why you are splitting on \\t in your complete.txt file, here is your code optimized:

ids = {}
with open('/Users/Zebrafish/Desktop/ASHISH/IDs.txt') as f:
    for line in f:
       if len(line.strip()):
           # This makes sure you skip blank lines
           id,start,end = line.split('\t')
           ids[id] = (int(start),int(end))

# Here, I assume your `complete.txt` is a file with one long line.
with open('/Users/Zebrafish/Desktop/ASHISH/complete.txt') as f:
    sequence = f.readline()

# For each id, fetch the sequence "chunk:
for id,value in ids.iteritems():
    start, end = value
    print('{} {}'.format(id,sequence[start-1:end]))

Answer 2

3MB is not huge (on a computer that can run Windows). Just load the second file into memory as a single string, to get the fragments:

# populate `id -> (start, end)` map
ids = {} 
with open(r"\Users\Zebrafish\Desktop\ASHISH\IDs.txt") as id_file:
    for line in id_file:
        if line.strip(): # non-blank line
           id, start, end = line.split() 
           ids[id] = int(start), int(end)

# load the file as a single string (ignoring whitespace)
with open("/Users/Zebrafish/Desktop/ASHISH/complete.txt") as seq_file:
    s = "".join(seq_file.read().split()) # or re.sub("\s+", "", seq_file.read())

# print fragments
for id, (start, end) in ids.items():
    print("{id} -> {fragment}".format(id=id, fragment=s[start:end]))

If complete.txt file doesn't fit in memory; you could use mmap , to access its content as a sequence of bytes without loading the whole file into memory:

from mmap import ACCESS_READ, mmap    

with open("complete.txt") as f, mmap(f.fileno(), 0, access=ACCESS_READ) as s:
    # use `s` here (assume that indices refer to the raw file in this case)
    # e.g., `fragment = s[start:end]`

Answer 3

Remove the line:

seqnew = seq.split("\t") 

Just do:

retrieved = seqnew[int(start):int(end)]

will get the sub-string you want.

Then you'll be able to:

print retrieved

Answer 4

Beware of the leading \\t in IDs.txt

>>> print "\ta\tb\tc"
        a       b       c
>>> "\ta\tb\tc".split("\t")
['', 'a', 'b', 'c']

i == 0 refers to an empty text rather than the gene ID.