kumar,
Looking at the quantity and structure of your data I think the search you are doing is going to be pretty slow - you will be doing 4504 * 398169 = 1,793,353,176 string searches.
Where does the seq data come from? Could you consolidate the pairs of lines into a single record? If you do that and extract the '399:559' portion, you could build a dict that maps '399:559' to the full record. Looking up '399:559' in the dictionary would be much, much faster than searching the entire list.
If you have multiple entries for '399:559' you could have the dict map to a list.
Kent
kumar s wrote:
len(x)
4504
x[1:10]
['454:494', '319:607', '319:608', '322:289', '322:290', '183:330', '183:329', '364:95', '364:96']
len(seq)
398169
seq[0:4]
['>probe:HG-U95Av2:1000_at:399:559; Interrogation_Position=1367; Antisense;', 'TCTCCTTTGCTGAGGCCTCCAGCTT', '>probe:HG-U95Av2:1000_at:544:185; Interrogation_Position=1379; Antisense;', 'AGGCCTCCAGCTTCAGGCAGGCCAA']
for ele1 in x:
for ele2 in seq: if ele1 in ele2: print ele2
probe:HG-U95Av2:31358_at:454:493;
Interrogation_Position=132; Antisense;
probe:HG-U95Av2:31358_at:319:607;
Interrogation_Position=144; Antisense;
How Do I WANT:
I want to print get an output like this:
probe:HG-U95Av2:1000_at:399:559;
Interrogation_Position=1367; Antisense;' TCTCCTTTGCTGAGGCCTCCAGCTT
probe:HG-U95Av2:1000_at:544:185;
Interrogation_Position=1379; Antisense; AGGCCTCCAGCTTCAGGCAGGCCAA
can any one please suggest what is going wrong in my
statements and how can I get it.
Thank you. Kumar
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