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Questions tagged [perl]

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votes
2answers
168 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 ...
1
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4answers
80 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 ...
1
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1answer
42 views

Pattern mining from a genomic sequence

I need to find the following pattern from a genomic sequence ...
1
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1answer
32 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 ...
2
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0answers
21 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
40 views

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

I'm trying to run Repeatmasker in Linux on the command line with: ...
4
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1answer
128 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 ...
1
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1answer
51 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 ...
-2
votes
1answer
73 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
39 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
vote
1answer
259 views

Error in installing Vep

I am trying to installing Vep on Linux but an error is permanent ...
1
vote
1answer
123 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
votes
1answer
50 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 ...
2
votes
2answers
82 views

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

I have a folder containing 500 files from different individuals: ...
4
votes
2answers
109 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
votes
3answers
74 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 ...
2
votes
2answers
235 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
votes
1answer
61 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 ...
4
votes
1answer
88 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 ...
3
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0answers
55 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 ...
1
vote
4answers
321 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, ...
2
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0answers
752 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: ...
-1
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1answer
65 views
0
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4answers
702 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 ...