Questions tagged [bioinformatics]
Use this tag for questions relating to common bioinformatics tasks performed on a *nix system. Things like manipulating/converting between standard biological text formats, extracting data of interest from such formats etc.
322 questions
1vote
3answers
66views
edit all the values in a specific column based on row numbers range
I have a PDB file (coordinates of atoms in a protein) on a Linux machine: ATOM 1 N GLY A 1 0.535 51.766 5.682 1.00 0.00 ATOM 2 CA GLY A 1 -0.712 50....
2votes
1answer
350views
how to pass environment variables to singularity exec
I have a BASH pipeline which at a point runs a Singularity container with singularity exec as follows: singularity exec --bind `pwd`:/folder --bind $d:/results <image>.sif <tool_command> -...
- 199
4votes
3answers
220views
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
1vote
4answers
117views
Find lines in Vim that start one way and that don't end in another way
I'm trying to use Vim to find, via /, lines that start and end in specific ways. In particular, I'd be looking for lines that start with the character > and without the string RNA at the very end. ...
6votes
3answers
927views
bash script quoting frustration
This problem is driving me crazy. From the command prompt I can enter this command and it works as expected (records where the INFO/RegionType tag contains the value Core are emitted in the output ...
- 69
2votes
5answers
321views
Grouping rows by categories avoiding repetition
I have a tab-separated file with two columns on a Linux machine. The first column contains names, the second column contains GO IDs (these are always of the format GO: followed by seven digits) ...
- 35
5votes
6answers
284views
subset columns from the 1st file using column names in 2nd file
I have two text files: 1st file is a Tab delimited file which looks like this: chrom pos ref alt a1 a2 a3 a4 10 12345 C T aa bb cc dd 10 12345 C T aa bb cc dd 10 12345 C ...
- 2,589
2votes
5answers
1kviews
Replace new lines with spaces using awk
I have a text file that I generated of all files in a directory. I'd like to use this file as input into a script that I have, but I need the text file to be formatted in a particular way to be parsed ...
1vote
5answers
123views
sed command to replace a word within a line following a pattern
I'm working with a file that looks like the following, containing with over 50,000 lines of gene IDs followed by their sequence: gene_A:3342234 CTCTTTCTTTTACGCCT gene_A:1244-5205 CTCTTTCTTTTACGCCT ...
2votes
5answers
545views
How to split a given column's string values in a text file
I have a text file on a Linux machine with two columns: Column 1 = id_no (most are 5, with some 6 digits long); Column 2 = genetic_markers (all are 50674 digits long); 12345 0102010205 54322 ...
1vote
4answers
158views
Remove everything in a third column but only keep specific text
I have a data set with three columns: https://drive.google.com/file/d/1gtCssfAXHxRjGfX8uTAaimGPWCA2cnci/view?usp=sharing Here are the first few lines: ID transcript_id go_description ...
1vote
4answers
485views
Retrieve the 1st and 5th column of a tab-separated file, convert the spaces in the 5th to tabs
I have a tsv file with tab-separated columns. I want to obtain the 5th column, which has space-separated values. Convert the space-separation to tab-separation and save as a new file. Attempt: cut -d&...
- 133
1vote
5answers
89views
How to count word from a column when consecutive cells are equal in a different column using shell script!
I'm trying to count the number of C_R and S_R in column 9 when consecutive cells in column 2, column 3, and column 1 are the same. The file is in bed format (tab-separated format). The original file ...
1vote
4answers
202views
Duplicate part of a line to another part
I would like to copy the first part (IxoscaEVm****t1_, without the '.p[number]') of the line starting with ">" and paste a before the last ":" of the same line. Input: >...
- 139
0votes
1answer
54views
Counting characters between grep searches
Is there a way I can use the grep command in conjunction with a series of other commands to find a character sequence (ie 'GAATTC' in a fasta file) and count how many characters are between each match?...
