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.
44
questions
3
votes
2
answers
62
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__♦
- 11.3k
0
votes
0
answers
70
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:
...
- 47
0
votes
0
answers
40
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 ...
3
votes
1
answer
131
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 ...
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 ...
- 41
3
votes
1
answer
58
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 ...
- 41
2
votes
1
answer
149
views
Installing modules in perl for Circos
Im trying to install the missing modules of Circos without success.
The error code is:
...
- 21
1
vote
1
answer
107
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 ...
- 51
2
votes
0
answers
87
views
Finding bioperl on cpanmetadb failed
I failed to install bioperl on debian in the following way:
...
- 453
2
votes
2
answers
133
views
Perl convert GFF3 file
I have the following GFF3 file which I would like to convert to ZFF file with the below script:
...
- 453
1
vote
0
answers
309
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 ...
1
vote
1
answer
37
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:
...
- 11
2
votes
1
answer
57
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 ...
- 185
3
votes
1
answer
47
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 ...
- 185
1
vote
1
answer
54
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 ...
- 13
1
vote
1
answer
247
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://...
- 31
0
votes
1
answer
553
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 ...
- 1,764
1
vote
2
answers
534
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:
...
- 43
0
votes
1
answer
1k
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 ...
- 109
3
votes
1
answer
824
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) ...
- 73
0
votes
2
answers
643
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 ...
- 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 ...
- 1,951
2
votes
1
answer
74
views
Pattern mining from a genomic sequence
I need to find the following pattern from a genomic sequence
...
- 109
1
vote
1
answer
42
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 ...
- 516
2
votes
0
answers
35
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, ...
- 21
3
votes
1
answer
333
views
"perl: warning: Setting locale failed." in RepeatMasker
I'm trying to run Repeatmasker in Linux on the command line with:
...
- 31
5
votes
2
answers
267
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__♦
- 11.3k
1
vote
1
answer
90
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__♦
- 11.3k
-2
votes
1
answer
99
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__♦
- 11.3k
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__♦
- 11.3k
1
vote
1
answer
1k
views
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:
...
- 119
2
votes
1
answer
92
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 ...
- 335
2
votes
2
answers
91
views
counting individuals with the present gene and absent gene for each population
I have a folder containing 500 files from different individuals:
...
- 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 ...
- 63
2
votes
3
answers
92
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
...
- 516
2
votes
2
answers
671
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 ...
- 1,764
2
votes
1
answer
152
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 ...
- 516
4
votes
1
answer
95
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
...
- 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 ...
1
vote
4
answers
557
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, ...
- 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:
...
- 29
-1
votes
1
answer
69
views
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 ...
- 524