I have a variation table (variation.txt) which is a very big file. The first column in the chromosome number and the second column is the position of the variation. I have a second file annotation.txt which has a list of 37,000 genes (1st column), their chromosome number(2nd column), their start and end coordinates (3rd and 4th column), followed by some details
I have to assign the variations (based on chromosome number and its position) to the genes. First, it should look for the **matching chromosome number** in both files, and if that matches, the coordinate of the variation should be within (including) start and end position of the gene. I have made an attempt to print the entries of variation table. I want to append the gene IDs also from annotation table in the first column of the output. How do I do that ?
Hello,
I am starting up an Xnest window and trying to place a program inside of it. I have the window inside of it now but it always spawns with the top left corner at (0, 0). I need to find a way to set the x and y coordinates to something other than (0, 0). I tried using the -geometry option... (1 Reply)
Hi
I have a file whose sample contents are shown here,
1.2.3.4->2.4.2.4 a(10) b(20) c(30)
1.2.3.4->2.9.2.4 a(10) c(20)
2.3.4.3->3.6.3.2 b(40) d(50) c(20)
2.3.4.3->3.9.0.2 a(40) e(50) c(20)
1.2.3.4->3.4.2.4 a(10) c(30)
6.2.3.4->2.4.2.5 c(10)
.
.
.
.
Here I need to search... (5 Replies)
Hi,
I have this problem on how to place the cursor in a text editor (for example: pico).
I made this script that would attach comments to a script file then open the script file,
I would like to know how to place the cursor in a specific place,
for example at the end of the comments,
... (1 Reply)
Hi there,
I'm having a problem trying to extract data from within a text file. I'm trying to extract this manually for a lack of better words.
I need any items that fall within latitude 36.5 to 39.5 and long -75.3 to -83.9
I have been doing this using cat neta.txt | grep '!38' and working... (6 Replies)
Hi guys. Can anyone tell me how to determine points between two coardinates. For example: Which type of command line gives me
50 points between (8, -5, 7) and (2, 6, 9) points
Thanks (5 Replies)
Hello all, this might be better suited for a bioinformatics forum, but I thought I'd try my luck here as well.
I have several tabular text files of DNA sequence reads that appear as such:
File_1.txt
>H01BA45XW GATTACAGATTCGACATCCAACTGAGGCATT
>H02BG78WR CCTTACAGACTGGGCATGAATATTGCATACC... (3 Replies)
Hi,
I would like to know how can I get the ID of a feature if its genomic coordinates overlap the coordinates of another file. Example:
Get the 4th column (ID) of this file1:
chr1 10 100 gene1
chr2 3000 5000 gene2
chr3 200 1500 gene3
if it overlaps with a feature in this file2:
chr2... (1 Reply)
Hello,
I extracted a list of files in a directory with the command ls . However this is not my computer, so the ls functionality has been revamped so that it gives the filesizes in front like this :
This is the output of ls command : I stored the output in a file filelist
1.1M... (5 Replies)
I have a file full of coordinates of the form:
37.68899917602539 58.07500076293945 57.79100036621094
The numbers don't always have the same number of decimal points. I need to reduce the decimal points of all the numbers (there are 128 rows of 3 numbers) to 2.
I have tried to do this... (2 Replies)
I am trying to compare/confirm the output of an script using the perl below, which does execute. However I can not seem to print $1 and $2 in each line of the input separated by a tab in each line of the output. The input file is quite large so I have only included a portion, but the format is the... (0 Replies)