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Search: Posts Made By: cmccabe
Forum: Shell Programming and Scripting 4 Weeks Ago
Replies: 10
Views: 319
Posted By cmccabe
Thank you very much, works great :).

Thank you very much, works great :).
Forum: Shell Programming and Scripting 4 Weeks Ago
Replies: 10
Views: 319
Posted By cmccabe
1-based coordinate system where the t in green is...

1-based coordinate system where the t in green is 166168510 and the t in blue is 166168623. For a sequence that has strand=+ in the > line, the above will always be true and as you move to the right...
Forum: Shell Programming and Scripting 4 Weeks Ago
Replies: 10
Views: 319
Posted By cmccabe
Thank you very much, works great.... very nice...

Thank you very much, works great.... very nice :).

------ Post updated at 02:17 PM ------

Looking into the data there are a couple of modifications that I am unsure how to incorporate. The...
Forum: Shell Programming and Scripting 4 Weeks Ago
Replies: 10
Views: 319
Posted By cmccabe
The line in green, specifically the tT{4}, is...

The line in green, specifically the tT{4}, is what I manually change to capture the different stretches of aA, tT, cC, gG stretches from 6-25. Is there a way to loop through the below possibilities,...
Forum: Shell Programming and Scripting 4 Weeks Ago
Replies: 10
Views: 319
Posted By cmccabe
Thank you @Aia, your perl is much more complete...

Thank you @Aia, your perl is much more complete than mine. Can the header be included with each sequence and if there is no repeat in that sequence Nothing Detected results? Thank you very much :).
...
Forum: Shell Programming and Scripting 08-18-2018
Replies: 10
Views: 319
Posted By cmccabe
Perl to adjust coordinates based on repeat string

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...
Forum: Shell Programming and Scripting 08-02-2018
Replies: 5
Views: 264
Posted By cmccabe
The same file was formatted with tab and space...

The same file was formatted with tab and space delimiters in it. Thank you very much :).
Forum: Shell Programming and Scripting 08-01-2018
Replies: 5
Views: 264
Posted By cmccabe
hgvs4variation.txt: ASCII text, with very long...

hgvs4variation.txt: ASCII text, with very long lines, but I am not sure what to do from here. Thank you :).
Forum: Shell Programming and Scripting 08-01-2018
Replies: 5
Views: 264
Posted By cmccabe
awk executes and works but only on copy of file

The tab-delimited file below using the awk produces a blank output. However, when I copy the same lines in file to a new document and execute the awk I get the desired result.
The awk counts the...
Forum: Shell Programming and Scripting 07-02-2018
Replies: 4
Views: 467
Posted By cmccabe
Thank you all :).

Thank you all :).
Forum: Shell Programming and Scripting 06-21-2018
Replies: 4
Views: 467
Posted By cmccabe
Using awk to add length of matching characters between field in file

The awk below produces the current output, which will add +1 to $3. However, I am trying to add the length of the matching characters between $5 and $6 to $3. I have tried using sub as a variable to...
Forum: Shell Programming and Scripting 06-16-2018
Replies: 4
Views: 383
Posted By cmccabe
Thank you very much :).

Thank you very much :).
Forum: Shell Programming and Scripting 06-15-2018
Replies: 4
Views: 383
Posted By cmccabe
The awk works great... thank you. I found two...

The awk works great... thank you. I found two additional format types and commented your code to try and capture these two additional. However I don't think I am understanding it correctly. Would you...
Forum: Shell Programming and Scripting 06-14-2018
Replies: 4
Views: 383
Posted By cmccabe
awk to format each line by pattern

The four lines in the tab-delimeted input are a sample format from my actual data. The awk is meant to go line by line and check if a pattern is satisfied and if it is follow a particular format...
Forum: Shell Programming and Scripting 05-31-2018
Replies: 0
Views: 262
Posted By cmccabe
awk to reformat lines based on condition

The awk below uses the tab-delimeted fileand reformats each line based on one of three conditions (rules). The 3 rules are for deletion (lines in blue), snv (line in red), and insertion (lines in...
Forum: Shell Programming and Scripting 05-10-2018
Replies: 3
Views: 337
Posted By cmccabe
Thank you both very much :).

Thank you both very much :).
Forum: Shell Programming and Scripting 05-09-2018
Replies: 3
Views: 337
Posted By cmccabe
awk to create separate files but not include specific field in output

I am trying to use awk to create (in this example) 3 seperate text file from the unique id in $1 in file, if it starts with the pattern aa. The contents of each row is used to populate each text file...
Forum: Shell Programming and Scripting 04-18-2018
Replies: 2
Views: 180
Posted By cmccabe
Thank you very much :).

Thank you very much :).
Forum: Shell Programming and Scripting 04-17-2018
Replies: 2
Views: 180
Posted By cmccabe
awk to adjust text and count based on value in field

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...
Forum: Shell Programming and Scripting 03-28-2018
Replies: 2
Views: 283
Posted By cmccabe
Thank you very much :).

Thank you very much :).
Forum: Shell Programming and Scripting 03-22-2018
Replies: 2
Views: 283
Posted By cmccabe
awk to update file based on match in 3 fields using two files

Trying to use awk to store the value of $5 in file1 in array x. That array x is then used to search $4 of file1 to find aa match (I use x[2] to skip the header in file1). Since $4 can have multiple...
Forum: Shell Programming and Scripting 02-22-2018
Replies: 2
Views: 367
Posted By cmccabe
Thank you very much :)

Thank you very much :)
Forum: Shell Programming and Scripting 02-22-2018
Replies: 2
Views: 345
Posted By cmccabe
Thank you very much :).

Thank you very much :).
Forum: Shell Programming and Scripting 02-20-2018
Replies: 2
Views: 345
Posted By cmccabe
awk to update file with sum of matching fields in another file

In the awk below I am trying to add a penalty to a score to each matching $1 in file2 based on the sum of $3+$4 (variable TL) from file1. Then the $4 value in file1 is divided by TL and multiplied by...
Forum: Shell Programming and Scripting 02-19-2018
Replies: 2
Views: 367
Posted By cmccabe
awk to calculate difference of split and sum the difference

In the awk I am trying to subtract the difference $3-$2 of each matching $4 before the first _ (underscore) and print that value in $13.
I think the awk will do that, but added comments. What I am...
Showing results 1 to 25 of 500

 


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