10
No, there is currently no GFF support in biopython.
However, you can read in GFF files into python using this package, gffutils. There are also a few other packages to read/write GFF files, like gff3.
9
Entrez Direct is perfect for this sort of thing. You can do something like this:
$ esearch -db sra -query 'SRR390728' \
| efetch -format runinfo \
| cut -f1,12 -d,
Run,LibraryName
SRR292241,HS0798
SRR390728,HS0798
The runinfo table format has 47 fields including experiment accession, project accessions, bioproject and biosample identifiers and such. You ...
9
Alternatively, you can use the NCBI Entrez Direct UNIX E-utilities
Basically, you have to download the install file here: https://www.ncbi.nlm.nih.gov/books/NBK179288/bin/install-edirect.sh
In the terminal, install it using: source ./install-edirect.sh
Then, you can download your sequence by doing:
esearch -db nucleotide -query "NC_030850.1" | efetch -...
7
tl;dr: technical difficulties, or sex
For the gorilla, that genome is from a female gorilla (Kamilah the gorilla) so she doesn't have a Y chromosome.
For the chimp link, there is a visualization of the chromosomes that you can click on that takes you to the genome browser for the Y chromosome (see image). Notably, there is a more recent genome build that ...
6
Answers to this question can be found on biostars. To give you a short summary:
Faster way might be to use the parallel-fastq-dump, as suggested in this answer. I never tested that tool though, my own experience is that prefetch is more stable than fastq-dump command.
In that same post it seems that the Japanese mirror seems faster, don't know if that is ...
6
Do you mean the NCBI taxonomy IDs? If so, I've personally always preferred the way UniProt displays NCBI taxonomy, and it's easier to download IDs in mass.
For example, if you find E.coli's entry: https://www.uniprot.org/taxonomy/562
You can then click on "all lower taxonomy nodes", which will show all E.coli strains. If you click 'Preview first 10'...
5
The simplest would be using a count matrix (at the end of the link you have shared, section "Supplementary file"). For example GSE138651_Vagal_WholeNodoseSeq_raw.mtx.gz corresponds to "raw" count matrices obtained after mapping and counting the reads. This file, along with the GSE138651_barcodes.tsv.gz and GSE138651_genes.tsv.gz can be used to "read" the ...
5
I would just blast it. When blasting locally, you need to first make a database from your genome, so assuming you got the command-line version of blast installed you can do something like
makeblastdb -in my_study_genome.fa -dbtype nucl
blastn -max_target_seqs 10 -db my_study_genome.fa -evalue 1e-10 -outfmt 6 -query my_downloaded_gene_of_interest.fasta -out ...
4
It sounds like your easiest option is to just install blast on your local machine and set up the databases there. It really will only take a few minutes to blast 6,000 sentences against a yeast genome on a modern laptop. Any solution interfacing with web results or parsing the output will be painfully convoluted. There are executables for blast that will ...
4
Just wget or curl each as https://www.ncbi.nlm.nih.gov/nuccore/NC_030853.1?report=fasta&log$=seqview&format=text...
4
While I haven't found a way to limit the results to the canonical transcript only, you can get a list of genes, transcripts and their CDS lengths using Ensemble's BioMart. I have already set it up for you, you can see the results, and modify them, here (click on the "Results" link if you don't see them).
Essentially, you just need to go to BioMart, and
...
4
Samtools
Samtools is a toolkit that includes a binary called samtoools, which can be used to query a FASTA file — to extract a subsequence based on some coordinate range you specify.
If you do not have samtools installed, you need to add it to your computer. For OS X, you could use Homebrew, for example:
$ brew install samtools
For Ubuntu, you could use apt-...
4
In your sequence header you will see:
[location=complement(940023..940580)]
It's a reverse strand gene. Reverse complement the sequence, then search the genome sequence.
3
The page you link to is a GenBank Flat file, the default format used by GenBank. So, to get that format, which includes the join lines, use:
./efetch -db nuccore -id CP003820.1 -format gb
The join() lines give the different ways in which a sequence can be built from this gene. For example, one mRNA sequence produced by the locus you mention (CP003820) is:
...
3
eUtilities for dbSNP is in the process of being retired. See this post from NCBI. You may want to check out the new API.
From the NCBI Insights blog post:
Entrez search is available only for human. We will retire all Eutils report formats (RS docsum XML and ASN.1, FASTA, and FLAT text) later this year. Only eSummary XML report will be supported.
Batch Query ...
3
For downloading data from commandline use the E-utilities of NCBI.
3
use a XSLT processor (http://php.net/manual/en/class.xsltprocessor.php) with the following stylesheet.
<?xml version='1.0' encoding="UTF-8"?>
<xsl:stylesheet xmlns:xsl='http://www.w3.org/1999/XSL/Transform' version='1.0'>
<xsl:output method="html"/>
<xsl:template match="/">
<div>
<xsl:apply-...
3
Outline of solution:
get this file: ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt
filter for lines having "Complete Genome" in column 12
filter for lines having a taxid (column 6) that is a descendant of taxon id 1117 (phylum Cyanobacteria), you can use nodes.dmp from ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz
The file ...
3
You can download the information using this link:
I did it in R:
tab = read.delim("https://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=SRA059451&result=read_run&fields=run_accession,experiment_title,sra_ftp,sample_alias")
head(tab)
run_accession
1 SRR585697
2 SRR585700
3 SRR585726
4 SRR585727
5 SRR585728
6 ...
3
I haven't done any whole-genome STR analysis from NGS data myself, but are aware of others that have used lobSTR for this. There's also a recent paper [here] that compares a few different STR analysis packages (i.e. RepeatSeq, LobSTR, HipSTR, GangSTR). Here's the concluding paragraph:
In conclusion, all these tools are built to genotype STRs but
have ...
3
You'll want something like:
esearch -db sra -query SRX1596422 | efetch -format runinfo
This will produce a CSV output to the screen with columns containing the meta information available in SRA:
Run,ReleaseDate,LoadDate,spots,bases,spots_with_mates,avgLength,size_MB,AssemblyName,download_path,Experiment,LibraryName,LibraryStrategy,LibrarySelection,...
2
The general procedure is explained here:
First step is to search the Taxonomy database with the organism name. Accepted common names usually work at all taxonomic levels. Use the scientific name or formal name if no results are obtained with the common name.
In code:
from Bio import Entrez
Entrez.email = 'user@example.org' # Put your email here
def ...
2
As an alternative, you can use the NCBI Datasets CLI, in a two step process to generate a dehydrated dataset for later hydration:
# Download metadata for all Cyanobacteria
# And pull out accession for 'Complete' genomes
./datasets assembly-descriptors taxon Cyanobacteria --limit ALL \
| jq -r '.assemblies[].assembly | "\(.assembly_accession) \(....
2
You can use Entrez Direct for this as follows:
efetch -db protein -id YP_805528.1 -format gpc -mode xml | xtract -insd Protein EC_number
YP_805528.1 6.3.2.13
2
Here's a very crude script version, which should work without downloading fancy software tools. It will only work as long as the website stays in its current layout.
It extracts the particular <td> from the webpage, based on a nearby table link ID. and prints it out.
Note: This is brittle. It will only work for library names that fit in a single-...
2
I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model.
The only downside is that I believe it is no longer actively supported. It is however the package that the BioPython docs use generally. There are plans to properly incorporate GFF/GTF parsers in to BP in the not too distant future according to that link ...
2
Go to the main FASTA sequence page, view source, and get the "ncbi_uidlist" value. In this case, it's 1061361601
Use the ID in the query string to download directly:
https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id=1061361601&db=nuccore&report=fasta&retmode=text&withmarkup=on&tool=portal&log$=seqview&maxdownloadsize=100000000
...
2
Downloading entire genomes
The best way to download FASTA sequences for an entire genome is to search for the genome, for example Theobroma cacao genome in the NCBI Assembly portal and use the big blue Download button.
Downloading individual chromosomes
For a given assembly, if you want to download the FASTA sequences for a bunch of chromosomes, you can ...
2
A simple approach is to search for the gene name in NCBI Gene portal but this can miss a few cases and often include genes that are unrelated because the gene symbol is used by other unrelated genes as well.
For a cleaner dataset, you can use the NCBI Orthologs as follows. Search for human ALDP in the NCBI homepage with All Databases selected in the ...
2
It seems just like two different mirrors contains the same SRA archive. If you still doubt, you can download both (its have relatively small size) and compare their md5sum.
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