python dictionary, make every odd number line to key and even number line to value from a file

Question

Hi, I have a text file like this:

>NM_145914.2:212
TCTGATGGTAAAAGTCGAGGAGAAAGAAGA
>NM_000614.3:1086
ATTCAATTTAAAATCAGACTCTTTAGTTGA
>NM_012096.2:2808
CAGTTAAGGTTTCAAATTGTGGCAGGTGGT
>NM_173465.3:1682
GTGCGTCGGGTGAGAGAGGCCCCAGCGGCC
>NM_001198858.1:490
CAACCACCACAACCTGCTGGTCTGCTCGGT
......more lines in same style......

What I want is:

read from above file, make line 1,3,5,7 ... to dictionary keys and line 2,4,5,8... to dictionary values.

My code is:

query_dict = {}
nameAt = 1
sequenceAt = 2

while name in range(totalLines):
line1 = linecache.getline(filename, nameAt)
line2 = linecache.getline(filename, sequenceAt)

query_dict[line1] = line2
nameAt  = nameAt + 2        
sequenceAt = sequenceAt + 2

The code worked, but its very slow, as the minimal lines of my text file is 200,000 lines. does anyone have better method to do this?

Thanks very much.

==============added follow-up question==================

here is fastq format, with 4 lines per read (record):

@>NM_052972.2:11:1054:1780:889
CTTCGACATCTCCGGCAACCCCTGGATCTG
+>NM_052972.2:11:1054:1780:889
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@>NM_080660.3:12:914:1802:542
CCTGTATGGCTACTGCAACCTCAAGGATAA
+>NM_080660.3:12:914:1802:542
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@>NM_176814.3:712:2706:4242:98
ACAGAGTAAAAGAGAGGCTGACTTAATAAA
+>NM_176814.3:712:2706:4242:98
IIIIIIIIIIIIIIIIIIIIIIIIIIIIII
...... more lines in same style ......

i want to create a dictionary, the key is 1st line and the value is 2nd line in each 4 lines of record.

the dictionary would look like:

{'@>NM_052972.2:11:1054:1780:889':'CTTCGACATCTCCGGCAACCCCTGGATCTG', 
 '@>NM_080660.3:12:914:1802:542':'CCTGTATGGCTACTGCAACCTCAAGGATAA',
 '@>NM_176814.3:712:2706:4242:98':'ACAGAGTAAAAGAGAGGCTGACTTAATAAA',
 ..... more keys and values ......
}

thanks.

Answer 1

Something like this:

with open('filename') as f:
    query_dict = {line.strip():next(f).strip() for line in f}

Output:

>>> from pprint import pprint
>>> pprint(query_dict)
{'>NM_000614.3:1086': 'ATTCAATTTAAAATCAGACTCTTTAGTTGA',
 '>NM_001198858.1:490': 'CAACCACCACAACCTGCTGGTCTGCTCGGT',
 '>NM_012096.2:2808': 'CAGTTAAGGTTTCAAATTGTGGCAGGTGGT',
 '>NM_145914.2:212': 'TCTGATGGTAAAAGTCGAGGAGAAAGAAGA',
 '>NM_173465.3:1682': 'GTGCGTCGGGTGAGAGAGGCCCCAGCGGCC'}

Update:

with open('foo.txt') as f:
    dic = {}
    for line in f:
        dic[line.strip()] = next(f).strip()
        next(f);next(f)  #Drop next two lines
from pprint import pprint
pprint(dic)

Output:

{'@>NM_052972.2:11:1054:1780:889': 'CTTCGACATCTCCGGCAACCCCTGGATCTG',
 '@>NM_080660.3:12:914:1802:542': 'CCTGTATGGCTACTGCAACCTCAAGGATAA',
 '@>NM_176814.3:712:2706:4242:98': 'ACAGAGTAAAAGAGAGGCTGACTTAATAAA'}

Answer 2

>>> s = """>NM_145914.2:212
... TCTGATGGTAAAAGTCGAGGAGAAAGAAGA
... >NM_000614.3:1086
... ATTCAATTTAAAATCAGACTCTTTAGTTGA
... >NM_012096.2:2808
... CAGTTAAGGTTTCAAATTGTGGCAGGTGGT
... >NM_173465.3:1682
... GTGCGTCGGGTGAGAGAGGCCCCAGCGGCC
... >NM_001198858.1:490
... CAACCACCACAACCTGCTGGTCTGCTCGGT""".splitlines()
>>> {i: j for i, j in zip(s[::2], s[1::2])}
{'>NM_145914.2:212': 'TCTGATGGTAAAAGTCGAGGAGAAAGAAGA', '>NM_000614.3:1086': 'ATTCAATTTAAAATCAGACTCTTTAGTTGA', '>NM_001198858.1:490': 'CAACCACCACAACCTGCTGGTCTGCTCGGT', '>NM_012096.2:2808': 'CAGTTAAGGTTTCAAATTGTGGCAGGTGGT', '>NM_173465.3:1682': 'GTGCGTCGGGTGAGAGAGGCCCCAGCGGCC'}

Use itertools.islice if memory is an issue:

{i: j for i, j in zip(islice(s, 0, len(s), 2), islice(s, 1, len(s), 2))}

Answer 3

Or, instead of a dict-comp:

from itertools import izip

with open('somefile') as fin:
    lines = (line.strip() for line in fin)
    query_dict = dict(izip(lines, lines))

Answer 4

That's a FASTA file. Install Biopython (pip install biopython) and parse it:

from Bio import SeqIO

with open('filename.fasta', 'rU') as handle:
    for record in SeqIO.parse(handle, 'fasta'):
        print(record)

Just look at that readable output:

ID: NM_145914.2:212
Name: NM_145914.2:212
Description: NM_145914.2:212
Number of features: 0
Seq('TCTGATGGTAAAAGTCGAGGAGAAAGAAGA', SingleLetterAlphabet())
...