Questions tagged [perl]

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1answer
72 views

Finding common and unique data set by comparing two files based on their column and to split the columns multiple strings to print in output

I have very large sizes tab-delimited .vcf files and want to match these two / or 3 files based on their position and print to a new .csv file File structures: File_1: tab-delimited file (.vcf) ...
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2answers
41 views

how to use list of gene id to get cds sequence(cds fasta file have many annotation, only gene id: is same to query id)

i have a question when i want to extract cds sequence using gene id. but cds file is not just start with >gene is, it has many other annotation. the only same is star with gene: cds fasta: ...
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1answer
92 views

How to generate ultrametric phylogenetic trees?

I have generated rooted species tree with 1000 bootstraps by RAxML. Further, I need to generate ultrametric tree for the same. Therefore, Please suggest me how to generate ultrametric tree from the ...
1
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4answers
135 views

How I can change the name of multiple files at once in R or terminal?

I have 200 .vcf files in a folder with long names like LP6005409-DNA_E03_vs_LP6005408-DNA_E03.snp.pass.vcf How can I change the name of each file to, for ...
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2answers
236 views

How to loop multiple function in shell script?

I need to extract sequences one after another consecutively from a large fasta files (multiple fasta files) and each extracted files to be saved in new fasta file (I mean the first sequence extracted ...
2
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1answer
55 views

Pattern mining from a genomic sequence

I need to find the following pattern from a genomic sequence ...
1
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1answer
33 views

storing SNPs in the genotype file for each chromosome in a separate file

I have already asked this question in another forum but have not got an appropriate answer, so wondering if anyone here can help me? I have a big file with over 3 million columns (SNPs genotypes) and ...
4
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1answer
170 views

HDF5 and BioSQL solutions

I'm looking at better database/storage solutions for NCBI virus data, with all attributes particularly year and country of isolation, together with structural data, possible antibody data, T-cell data ...
2
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0answers
24 views

How to interprete PlasmidSeeker results concerning plasmids?

I've been interested in plasmid detection in bacterial genomes. I tried plasmidfinder and this software found only one plasmid in each of my two bacterial genomes. I was dubious about these results, ...
2
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0answers
74 views

“perl: warning: Setting locale failed.” in RepeatMasker

I'm trying to run Repeatmasker in Linux on the command line with: ...
1
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1answer
58 views

Multi-line efetch digging

I'm using efetch to dig out a middle "envelope" protein within a viral genome specifically within fasta format. The code below works but may not be robust for an entire database. Thus I want to ...
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1answer
79 views

How about BioMoose? [closed]

This is a silly post, but hope it makes a point. We have BioPerl (which never impressed me, in fact there isn't even a BioPerl tag), BioPython (which admittedly is impressive), and even now BioRust. ...
1
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2answers
48 views

awk for motif splicing from an amino acid alignment

I'm looking to splice out specific amino acid alignment positions as a continuous motif from an alignment (~15 000 sequences). The code is written in Perl (I agree not many developers now) but ...
1
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1answer
398 views

Error in installing Vep

I am trying to installing Vep on Linux but an error is permanent ...
2
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1answer
63 views

Error while performing “lift-over” of genomic coordinates between two species using Ensembl Compara API

I'm trying to convert coordinates between the reference mouse genome and CAST/EiJ mice strain. Since Ensebml already has alignment available in the browser, I decided to use Ensembl perl API to lift ...
1
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1answer
132 views

How to separate a microbial strain of MTB resistant and susceptible drugwise?

Im trying to classify my list into three type: XDR - A strain must be resistant to: ...
2
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2answers
85 views

counting individuals with the present gene and absent gene for each population

I have a folder containing 500 files from different individuals: ...
4
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2answers
127 views

Writing a perl script to holding information for two genes

Basically I have a perl script in which I have an array (where each element of the array references a hash) and need to be able to print the array with a dumper function. Thus I need to be able to ...
2
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3answers
82 views

assigning different characters to present and absent genes from blast output using perl or python

I have file called pangenome.txt which has only one column containing the names of the genes ...
4
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1answer
90 views

replacing SNPs with missing calls with a specific string

I have a big file containing 27 columns and nearly 6 million rows. The following is a little example of my file ...
2
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2answers
281 views

Parse out exon coordinates from bed file for each gene

This is my bed file for all the exon coordinates I want to take out all the exons of a given gene. Let say I have gene in chr 1 which starts from chr1 11868 12227 ...
2
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1answer
80 views

how to count the number of each allele of CNVs?

I have a bunch of files (vcf format) each containing site and sample annotations of a copy number variant (following example is part of one of my files, I am showing 11 individuals but they are nearly ...
1
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4answers
383 views

Convert population allele count into population allele frequency by using Perl or Python (translate available Bash into Perl or Python)

I already know the Bash AWK solution and also R code for the question that I am asking. But, my file is so big and with R it takes very long time and I am afraid of AWK's mistake for this computation, ...
3
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0answers
56 views

Trying to show the gaps of each seq on bio::Graphics after converting clustalw

I've been having trouble for a while with this and have been trying to get this on my own, but I can't. I'm trying to display the gaps using Bio::Graphics after ...
2
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0answers
1k views

Error “Can't locate List/MoreUtils.pm in @INC” when I run update_blastdb.pl

I encoutered some technical problem when learning BLAST as below: After I use conda install blast to install ncbi-blast, and run the command: ...
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1answer
67 views
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4answers
825 views

For what bioinformatics tasks is Biopython more adapted than Bioperl?

Are there any advantages to learning Biopython instead of learning Bioperl? Ideally, we would learn both, but someone starting out in bioinformatics may have to choose what to learn first depending ...