In the file below I am trying to count the given repeats of A,T,C,G in each string of letters. Each sequence is below the > and it is possible for a string of repeats to wrap from the line above. For example, in the first line the last letter is a T and the next lines has 3 more. I think the below would work, but I am also trying to count the position range of the repeat using the range=, where the first # represents the leftmost (in the first line that is aaa) and the second # rightmost (in the first line that is taa). So using the 4T as an example the output is in the example output.
The t{4} is the repeat that can change, for example if I am after 7g then that would be g{7}... the lower case letters in the sequence are counted along with the capital letters if they satisfy the criteria. I think both would be captured in the order there are seen, as that is important to know. For example, 4t occurs at chr2:166911127-166911130... even though there are 6t in that strech only the 4t satisfy the criteria and are counted. An example output is in the output for two sequences. Thank you .
the first T is 50 in so that is added to the 166911123 and that is the new value after the : and the last T is 53 so that is added to the 166911123 and that is the new value after the -.
perl
Code:
perl -076 -nE 'chomp; s/(.+)// && say qq{>$1}; s/\s//g; say $1 while /(t{4})/gi' file
Hello Unix gurus,
I have a gzipped file where each line contains 2 street addresses in the US. What I want to do is get a count for each state that does not match.
What I have so far is:
$ gzcat matched_10_09.txt.gz |cut -c 106-107,184-185 | head -5
CTCT
CTNY
CTCT
CTFL
CTMA
This cuts... (5 Replies)
here is what i want to achieve... consider a file contains below contents. the file size is large about 60mb
cat dump.sql
INSERT INTO `table1` (`id`, `action`, `date`, `descrip`, `lastModified`) VALUES (1,'Change','2011-05-05 00:00:00','Account Updated','2012-02-10... (10 Replies)
I am a novice writing perl scripts so I'd appreciate any help you guys can offer.
I have a list of 100 words in a file (words.txt) and I need to find them in a second file (data.txt). Whenever one of these words is found I need to write that line to a third file (out.txt) and then continue... (1 Reply)
Hi,
I would like to have the length of a segment based on coordinates of its parts.
Example input file:
chr11 genes_good3.gtf aggregate_gene 1 100 gene1
chr11 genes_good3.gtf exonic_part 1 60
chr11 genes_good3.gtf exonic_part 70 100
chr11 genes_good3.gtf aggregate_gene 200 1000 gene2... (2 Replies)
Use and complete the template provided. The entire template must be completed. If you don't, your post may be deleted!
1. The problem statement, all variables and given/known data:
My goal to find how many requests in 14 days from weblog server. I know to cat a weblog file to wc -l to find the... (8 Replies)
I am trying to add a condition to the below perl that will capture the GTtag and place a specific string in the last field of each line. The problem is that the GT value used is not right after the tag rather it is a few fields away. The values should always be 0/1 or 1/2 and are in bold in the... (12 Replies)
Trying to output a result that uses the data from file to combine and subtract specific lines. If $4 matches in each line then the last $6 value is added to $2 and that becomes the new$3. Each matching line in combined into one with $1 then the original $2 then the new$3 then $5. For the cases... (4 Replies)
I am trying to output a tab-delimited result that uses the data from a tab-delimited file to combine and subtract specific lines.
If $4 matches in each line then the first matching sequential $6 value is added to $2, unless the value is 1, then the original $2 is used (like in the case of line... (3 Replies)
The below awk executes as is and produces the current output. It isvery close but what Ican not seem to do is add the -exon..., the ... portion comes from $1 and the _exon is static and will never change. If there is + sign in $4 then the ... is in acending order or sequential. If there is a - in... (2 Replies)
08-18-2018
.