All Questions
11 questions
4
votes
3
answers
220
views
Add columns from variable number of files to base file
I'm dealing with a series of bed files, which look like this:
chr1 100 110 0.5
chr1 150 175 0.2
chr1 200 300 1.5
With the columns being chromosome, start, end, score. I have multiple different files ...
- 245
0
votes
2
answers
136
views
AWK: If two key columns match between files, add the 16th column of one file to the matching row of the other while keeping non-matching rows
I have two tab separated files (FileA.tsv and FileB.tsv).
FileA.tsv
id
graph
circle
several columns...
length
196-0
196
0
----
12874
195-1
195
1
----
12874
56-0
56
0
----
3349
115-1
115
1
----
5297
...
- 3
3
votes
2
answers
765
views
How to display the difference between two DNA Sequences via command line tools
I have the following problem:
My data sheet looks like this
AAAGGGTTT AAAGGG
AAAGGGCCC GGGCCC
and I want to display the difference between the two sequences in the third row like this
AAAGGGTTT ...
- 31
1
vote
1
answer
369
views
for loops to grep multiple texts from parent file to multiple files in single command
I have 29 fasta files (.fa as extension) named and stored sequences according to their genes.
(Example: ribosomal protein L1, ribosomal protein L6P/L9E,...)
There were a total of 722 species ...
- 193
1
vote
2
answers
451
views
How to match a column from File1 to get its corresponding fasta sequences in File 2?
May I kindly ask how to match all values of the first column in File with the line text in File 2 so I can copy the fasta sequences of all Object ID in File 1?
File 1.csv file
Object_ID, Length, ...
- 11
-1
votes
1
answer
4k
views
converting fasta file to plain text
how to convert fasta format with ">" to plain text file
ex.
input :fasta file
>1M14
GATCGGACTAGCTAA
output :plain text file
GATCGGACGAGCTAA
2
votes
1
answer
634
views
How to find characters between 2 strings and append them with some text to end of line?
I am dealing with fasta files having lines such as:
\>97977-100;sample=Samp1
TAATGATGATTTGT
\>97978-60;sample=Samp2
AACATTCAACGCGGTCGGTGAGTA
\>97979-30;sample=Samp3
...
20
votes
6
answers
8k
views
Running a command on many files
I've got a folder with many files (xyz1, xyz2, all the way up to xyz5025) and I need to run a script on every one of them, getting xyz1.faa, xyz2.faa, and so on as outputs.
The command for a single ...
- 453
-1
votes
2
answers
67
views
Replace characters in a hapmap data set
I am thinking to use a bash code to solve the following issue in my data.
Considering the bellow data set in hapmap format in which I need to replace some characters (letters in this case) based on ...
- 67
4
votes
2
answers
9k
views
Nested 'awk' in a 'while' loop, parse two files line by line and compare column values
I need some help with a combination of awk & while loop.
I have two simple files with columns (normal ones are very large), one representing simple intervals for an ID=10(of coding regions(exons),...
- 65
5
votes
2
answers
8k
views
counting multiple patterns in a single pass with grep?
I've written a grep loop to iteratively count DNA trinucleotides within a gzipped DNA fasta file containing DNA sequences e.g.
declare -a tri=(AAA AAC AAG AAT CAA .. etc)
for i in ${tri[@]}
do
...
