Questions tagged [perl]

Generally refers to Perl5 and is a much loved computer language of exceptional beauty and simplicity. It is the hallmark of exceptional character.

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Trouble Running VEP in Conda Environment Due to Perl DBD::mysql Error

Hello StackExchange Community, I am currently facing issues with running the Variant Effect Predictor (VEP) and vcf2maf in a Conda environment due to a Perl-related error. Installation Steps: I ...
qiuting Zhang's user avatar
3 votes
2 answers
82 views

Remote NCBI's Blast Perl API: maximising hits returned via command line

Question and Background I'm using NCBI's Blast Perl API to interrogate Genbank for example blastp. I don't get the throughput using their point and click web stuff. ...
M__'s user avatar
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0 votes
0 answers
76 views

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: ...
MTG's user avatar
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0 votes
0 answers
42 views

What tool(s) can I use to use a .faa file to feed into JSMol?

JSMol, the molecular modelling software, requires PDB file format to work and render the graphics. Currently, I am writing an annotation software - backend in Perl - that takes in a .faa file (fasta ...
Harish Prabhakar's user avatar
3 votes
1 answer
216 views

Barrnap Bacterial rRNA Predictor script permission denied error when running Prokka

I am trying to run the Prokka annotation tool on my linux machine and have installed Barrnap and added it to $PATH and given the folder chmod 777 permission. However, when running Prokka, it gives the ...
Harish Prabhakar's user avatar
2 votes
1 answer
36 views

Running Bionano´s HybridScaffolding from the command line [Error: align0.stdout]

as the title says I´m trying to run Bionanos HybridScaffolding from the command line rather than using their own software interface. This is commercial software to primarily to identify genomewide ...
snakelake's user avatar
3 votes
1 answer
62 views

Parsing pre-2007 SMILES string

How would one parse the SMILES string BrC[2]:C[3]:C(:CH:CH:CH:@2):CH:CH:CH:CH:@3 I rely on tools like rdkit and ...
Ryan Park's user avatar
2 votes
1 answer
178 views

Installing modules in perl for Circos

Im trying to install the missing modules of Circos without success. The error code is: ...
Ale's user avatar
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1 vote
1 answer
135 views

BPGA error: there was no protein data in file

I'm trying to do pan-genome analysis using BPGA and I face this error: This error didn't show up in the other data set where all the .gbk is downloaded from NCBI. This .gbk file is our own data and ...
raysteven's user avatar
2 votes
0 answers
149 views

Finding bioperl on cpanmetadb failed

I failed to install bioperl on debian in the following way: ...
user977828's user avatar
2 votes
2 answers
154 views

Perl convert GFF3 file

I have the following GFF3 file which I would like to convert to ZFF file with the below script: ...
user977828's user avatar
1 vote
0 answers
399 views

tmhmm installation and running

I am trying to predict transmembrane protein using tmhmm-2.0c. According to Package instruction, I have changed the path of perl inside the program like as ...
Kishor Kumar Sarker's user avatar
1 vote
1 answer
41 views

Using txt file to query Ensembl API

I am trying to use an external file with a list of gene names to query the ENSEMBL IDs using the perl API. This script works: ...
user45678789's user avatar
2 votes
1 answer
74 views

How to know if ID correspond to nucleotide sequence or protein with a script

I have a text file that contains a list of IDs (314 sequences): AVP78031.1 AVP78042.1 ATO98108.1 ATO98120.1 ATO98132.1 ... My goal is to make a script (maybe using ...
Someone_1313's user avatar
3 votes
1 answer
54 views

Tajima-Nei Distance estimate with BioPerl

I have been trying to estimate Tajima-Nei distance for my data (link below). The output is s phylogenetics distance (pairwise) matrix which accommodates a detailed transition transversion and the ...
Someone_1313's user avatar
1 vote
1 answer
56 views

how to repeat records in fastq n times efficiently?

How to iterate/repeat a record n times in a fastq file using bioawk? I wrote a python code using biopython, but it is very very slow. So, I am wondering if I can get some help by using bioawk. Thank ...
Xiaofei Wang's user avatar
1 vote
1 answer
293 views

Can't locate object method "new" via package Bio::Tools::Primer3

Hi there I am still a novice at this. I'm trying to run this perl script called FullSSR https://sourceforge.net/projects/fullssr, by following the instructions in their 'README.TXT' https://...
ShawnC's user avatar
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0 votes
1 answer
646 views

Removing stop codons from alignment file for dn/ds calculation

This is one of the question which is very similar to my problem or almost same to my problem I ran with dummy data nucleotide alignment and the amino file it works perfectly fine,i can run the dn/ds ...
kcm's user avatar
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1 vote
2 answers
671 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: ...
user8692's user avatar
0 votes
1 answer
2k views

How to generate ultrametric phylogenetic trees?

This question has also been asked on Biostars I am going to use ultrametric tree for downstream analysis. I would like to see use the ultrametric tree for Ranger-DTL for infer gene family evolution by ...
Kumar's user avatar
  • 109
3 votes
1 answer
921 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) ...
Nitha's user avatar
  • 73
0 votes
2 answers
649 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 ...
Kumar's user avatar
  • 109
1 vote
4 answers
2k 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 ...
Zizogolu's user avatar
  • 2,148
2 votes
1 answer
74 views

Pattern mining from a genomic sequence

I need to find the following pattern from a genomic sequence ...
Kumar's user avatar
  • 109
1 vote
1 answer
44 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 ...
Anna1364's user avatar
  • 516
2 votes
0 answers
36 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, ...
El Niño's user avatar
3 votes
1 answer
361 views

"perl: warning: Setting locale failed." in RepeatMasker

I'm trying to run Repeatmasker in Linux on the command line with: ...
RNAdey's user avatar
  • 31
5 votes
2 answers
287 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 ...
M__'s user avatar
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1 vote
1 answer
91 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 ...
M__'s user avatar
  • 12.3k
-2 votes
1 answer
100 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. ...
M__'s user avatar
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1 vote
2 answers
94 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 ...
M__'s user avatar
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2 votes
1 answer
2k views

Error in installing Vep

I am trying to installing Vep on Linux but an error is permanent ...
Zizogolu's user avatar
  • 2,148
1 vote
1 answer
134 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: ...
Safina A.R's user avatar
2 votes
1 answer
94 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 ...
Siddharth's user avatar
  • 345
2 votes
2 answers
92 views

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

I have a folder containing 500 files from different individuals: ...
Anna1364's user avatar
  • 516
4 votes
2 answers
158 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 ...
code_pink's user avatar
2 votes
3 answers
96 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 ...
Anna1364's user avatar
  • 516
2 votes
2 answers
735 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 ...
kcm's user avatar
  • 1,804
2 votes
1 answer
154 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 ...
Anna1364's user avatar
  • 516
4 votes
1 answer
96 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 ...
Anna1364's user avatar
  • 516
3 votes
0 answers
59 views

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

I want a box representing each sequence, positioned as they are in the alignment and with gaps shown as breaks in the each box. I've been having trouble for a while with this and have been trying to ...
Jeffery Rosario's user avatar
1 vote
4 answers
574 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, ...
Anna1364's user avatar
  • 516
2 votes
0 answers
2k 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: ...
Oliver's user avatar
  • 29
-1 votes
1 answer
70 views

Bioperl - how can i print first result of search sequence per iteration?

...
MTG's user avatar
  • 147
1 vote
4 answers
1k 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 ...
jaslibra's user avatar
  • 524