Questions tagged [bash]
Use this tag to refer to the questions related to the Linux and Unix shell abbreviated as bash (Bourne Again SHell). It has notable programmatic strengths over C shell (csh) and touch C shell (tcsh)
112
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Filtering columns from large file based on a column list
I have list of samples as a txt file and want to only keep these samples from this large file; column name is samples name in the large file.
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2
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0
answers
33
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Racon: empty overlap set!
Not sure if anyone can help me with a Racon issue as the developers are not very responsive on GitHub. I am trying to assemble a genome without a reference. I first did basecalling using dorado, then ...
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2
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74
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How to calculate average from a column when consecutive cells are similar in different columns?
I wonder how can I calculate the average of column 7 (WPS_win) 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 ...
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0
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72
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Old program make error ProtDeform
Im trying to run ProtDeform on ubuntu 20.04
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125161/
I need scoring function :/ to my project
But error occurs:
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2
votes
1
answer
83
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Analysis of RNA sequencing with zUMIs
I wrote the .yaml file which was according the instruction from zUMIs:
...
0
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1
answer
85
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A bash script for running on a bunch of bam files
I have some bam files in this directory
/data/Continuum/WES/results/
I want to run GATK mutation calling over bam files
I ...
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1
vote
1
answer
31
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Create bam from separate sam and header
If I have multiple SAM files without header, and a header saved in a separate file, how do I convert that to a BAM file?
One solution is to create intermediate files:
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4
votes
2
answers
184
views
How can I give different names to files in a directory with a for loop in a bash script?
I'm expecting to get 17 different paired-end fastq files (34 in total), so I want to make a bash script to just run my code through all the fastq files in a directory at once. How can I change the ...
0
votes
1
answer
49
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How can I change all text in a .tsv file to 1, except the first three fields?
I want to convert a .tsv file table in binary format (1 and 0). In which all cells containing text would become 1 and blank cells would become ...
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1
vote
3
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243
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How to join multiple large .tsv (> 20 GB, bed file) files by two identifier?
This question has also been asked on Biostars
I wonder how can I join multiple large .tsv files (over 20 GB each) by using two identifiers (columns) which I used to do using the ...
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1
answer
29
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Variant Filtering Using AnthonyOzerov/variant-filtering Github Repository And Python Errors
I am using the following Github repository that I cloned. One apparent issue is that it is using an old/defunct link for the phenotype_to_genes.txt that is no longer active and after several tries I ...
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2
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175
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Singularity And CNV Kit
I would like to try an use Singularity with CNV kit as the HPC I use seems to work better with Singularity:
Initial Attempt:
...
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2
votes
1
answer
82
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CNV Kit ` from . import commands ImportError: cannot import name 'commands' from '__main__'`
I am trying to run some code for my colleague in bash
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3
votes
3
answers
230
views
Easier / lazy way to convert an existing bash pipeline to nextflow pipeline?
Not going to lie, my head hurts when I read the NextFlow documentation (No dig on the documentation, I think my head is losing its processing capacity lol).
I had written a pipeline in Bash, ...
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2
votes
4
answers
564
views
Parallelize or qsub a bash script
I have a bash script that I would like to parellelize to run on multiple nodes. My goal is to run my python sample_script.py script on pairwise comparisons of samples to see if their variants are a ...
- 21
2
votes
1
answer
94
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Dealing With Manta Limitations
I am trying to figure out a way to remove the limiting factors that Manta says it cannot handle. To quote from the Manta page:
The following limitations exist on the input BAM or CRAM files provided ...
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3
votes
1
answer
44
views
Passing strings for password, email authentication and download link
Hi I am downloading the data from a website which requires authentication of email_id and password before the download. They then provide the download link which is used to download dataset. This ...
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2
votes
1
answer
99
views
Manta "--exome: command not found"
I am using Manta (https://github.com/Illumina/manta/blob/master/docs/userGuide/README.md) but whenever I try to specify the --exome command using the following code ...
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0
votes
1
answer
59
views
Replace a string in a column of a text file based on matching string listed in another file using linux
I have multiple sets of files, so I grepped the list from a column in a seperate file such as file1.txt. I want to change all other files by using this file1.txt based on a matching string.
for ...
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2
votes
1
answer
81
views
Default placeholder for missing fields doesn't work with block in xtract tool
I am using the xtract tool of the Entrez Direct (EDirect) package of NBCI. I have a list of Accession Numbers:
...
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1
vote
4
answers
184
views
How to remove empty files from a directory?
I have a directory of FASTA files, some of which are empty (placeholders that were output from a pipeline) and I would like to delete the empty files using a for loop on the command line.
From what I ...
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votes
4
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472
views
How to rename a file based on a directory name?
I have a lot of FASTA files that I recently scaffolded with RagTag. The output of RagTag includes a directory for each sample and the corresponding FASTA file written as "ragtag.scaffold.fasta&...
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3
votes
1
answer
235
views
Run nextflow pipeline multiple times depending on length of a list
This question was also asked on Stack Overflow
I have a Nextflow pipeline that runs a BUSCO search on input data, returns the output and then creates a report based on the output. One of my parameters ...
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1
vote
1
answer
53
views
Problems with BED format for ClinCNV
I have some problems with ClinCNV(https://github.com/imgag/ClinCNV):
I made a BED file from a BAM, then i made a GC count with ngs-bits (link: https://github.com/imgag/ngs-bits )
The main idea of ...
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3
votes
1
answer
105
views
How to remove double '/' from file path, bash script
I'm using the following script to detect strandedness of my paired end RNA-seq data.
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2
votes
2
answers
591
views
How to wget a gff from NCBI database?
Say I want to use wget to download a gff file for the X chromosome of release 5.57 of the Drosophila melanogaster genome. The NCBI page with the gff file for just this is here.
However, I do not see ...
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vote
3
answers
83
views
eQTL data extraction from database JSON file
I have a long list of JSON data, with repeats of contents similar to followings.
Due to the original JSON file is too long, I will just shared the hyperlinks here. This is a result generated from a ...
- 13
2
votes
1
answer
110
views
Error Registering Job Definition AWS
I am in the process of creating a bioinformatics pipeline and I am currently trying to setup the AWS infrastructure for which it will run.
The script I am running to setup the AWS batch job looks like ...
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1
vote
2
answers
132
views
Is there an equivalent of Entrez queries for local BLAST?
I have been having some trouble with running command line BLASTn remotely. Therefore, upon recommendations, and considering I have >100 searches planned, I am considering just downloading the nt ...
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1
vote
1
answer
161
views
Running a Python Script from a bash script on multiple input files across different directory paths
I am in the process of writing up a bash script that runs three bioinformatics tools and then executes a python script. This python script compiles some of the data from the informatics tools output ...
- 101
3
votes
2
answers
364
views
Remote blastn - what is breaking my (bash) loop?
I am trying to search the NCBI non-redundant database for sequences similar to a few other (~40) sequences that I already have.
So I've tried running blastn remotely, and looping through multiple ...
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4
votes
0
answers
123
views
Write a bash script to run gatk, fix errors with input, and rerun until completion
I have a bam file that I want to run through GATK's SplitNCigarReads tool. Because of the way the bam file was generated, the program will often fail, with an error message stating:
...
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3
votes
2
answers
83
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bash script for interproscan REST
hey i have the problem with bash script. It should run interproscan REST
Im green in bash scripting. I found this script on the web:
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votes
0
answers
49
views
Is there a way antiSMASH can be used to screen a large number of genomes just for one type of biosynthetic gene cluster?
When we use antismash command with the genome sequence file as follows:
antismash GCA_002095535.1_ASM209553v1_genomic.gbff
it screens the genome for all the ...
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3
votes
4
answers
897
views
How can I add a ";" at the end of each fasta header line in a file?
I have a large fasta file with RNA sequences. I need to add a ; at the end of each header line (lines beginning with >) in ...
2
votes
1
answer
700
views
How do I use bash for loops to loop through a WDL Array?
Within the example below a WDL array of strings, test is defined as "a","b","c","d" the ...
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2
votes
2
answers
134
views
Mapping to assemblies in subdirectories
I am performing a bash loop one liner:.
for k in */Assembly/*/*.fastq; do minimap2 -ax map-ont assembly.fasta $k > mapping.sam; echo $k; done
The file hierarchy ...
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2
votes
1
answer
227
views
Python argparse error
Hi I am trying to use this python script (running with bash script) to do my analysis. I am getting the following error:
File "my_python_script.py", line 33
logging.info("Reading input2 ...
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1
vote
2
answers
245
views
Permutations of 4 amino acid sequence oligopeptide
I have an assignment for a project to build a tetrapeptides library to screen against some target enzymes in silicon.
I am looking for a script to construct about 160000 tetrapeptide from the 20Amino ...
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votes
1
answer
11k
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curl: (22) The requested URL returned error: 400 Bad Request when using entrez direct
I've just dowloaded entrez direct on my Mac and I was trying to perform some simple queries like:
...
1
vote
2
answers
69
views
Is there a way to calculate the Ka/Ks value in R/unix?
I am investigating the rate of synonymous non synonymous substitutions and would like to find the Ka/Ks value also known as dn and ds between multiple alleles? I want to investigate multiple alleles ...
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2
votes
1
answer
43
views
Automatize classical debugging in a bash script? (normal debugging by hand)
And thanks in advance. I am debugging a text file which is the one the two inputs on the program RGmatch https://bitbucket.org/pfurio/rgmatch/src/master/.
The code works. Is that some records give ...
1
vote
2
answers
396
views
Retain only part of a file name and fasta header in fasta directory
I have a MainDirectory/hundreds_of_subdirectories/thousands_of_fastas structure. For each fasta in the bottom level, I am trying to change the file name as well as ...
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vote
0
answers
21
views
Nucleotide Frequency - HOMER?
I'm trying to find the frequency of UA dinucleotide in a bed file. I want to convert the bed file to FASTA, count all the UA dinucleotides up, then divide by the total length of the FASTA file.
Also, ...
0
votes
1
answer
917
views
Cellranger gives error
I am trying to run cellranger but I get fastq permission denied error
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3
votes
2
answers
58
views
Calling for one specific SNP from multiple sequencing runs
Just learning the basics of bioinformatics and bash shell scripting.
Is there a correct way to search for a specific allele with one or even multiple sequencing runs? I am searching for prevalence of ...
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1
vote
1
answer
170
views
how to sort and join two files based on First Column Id
I have got two files large files like this in Tab-delimited format, trying to merge in R, do we need to sort the file before merging?
...
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votes
3
answers
2k
views
Removing duplicate FASTA sequences based on headers with Bash
I used the following command to remove duplicate FASTA sequences based on the header sequence:
...
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votes
2
answers
165
views
Filter rows of VCF file for Match=EXACT?
How do I remove rows in a VCF file on 1kGenome column, where Match=EXACT using bash ?
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votes
2
answers
82
views
Print specific columns in a matrix on the basis of sample id's in the header
I have a matrix file (expression.txt) in which the first column is a gene_id and from the second column the sample id's start. This matrix has 20,000 columns with sample id's corresponding to ...
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