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 ?
Please explain how this line
made it into the desired ouput - there is no connection between Solyc00g005060.1.1 and SL3.0ch02 in your annotation file, but it exists for the Solyc00g005000.3.1 and SL3.0ch02 pair. And, why isn't Solyc00g005050.3.1 / SL3.0ch00 mentioned? Shouldn't that match the third variation line?
Howsoever, pls try and report back
Its results match the desired output except for the two mentioned lines plus, mayhap, the field separators (which weren't specified, btw).
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)
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)
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)
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 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 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)
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,
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
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)
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)