BioInformatics Tools
Installation
python3 -m pip install bioinfo-toolset
Usage
bit --help
Example
bit vep -l ENST00000257430.9:c.3927_3931del
Result for ENST00000257430.9:c.3927_3931del
GRCh38: ENST00000257430.9:c.3927_3931del -> 5:112839521-112839525 (AAAGA > -)
GRCh37: ENST00000257430.9:c.3927_3931del -> 5:112175218-112175222 (AAAGA > -)
assembly_name : GRCh38
id : ENST00000257430.9:c.3927_3931del
seq_region_name : 5
start : 112839521
end : 112839525
allele_string : AAAGA/-
strand : 1
most_severe_consequence : frameshift_variant
Colocated variants (1):
id : COSV57321812
seq_region_name : 5
start : 112839521
end : 112839525
allele_string : COSMIC_MUTATION
strand : 1
somatic : 1
---
Transcript consequences (8):
transcript_id : ENST00000257430
gene_symbol : APC
gene_id : ENSG00000134982
hgnc_id : HGNC:583
amino_acids : EKI/DX
consequence_terms : ['frameshift_variant']
protein_position : 1309-1311
transcript_name : EKI1309-1311DX
---
transcript_id : ENST00000502371
gene_symbol : APC
gene_id : ENSG00000134982
hgnc_id : HGNC:583
consequence_terms : ['3_prime_UTR_variant', 'NMD_transcript_variant']
protein_position : N/A
transcript_name : N/A
---
transcript_id : ENST00000504915
gene_symbol : APC
gene_id : ENSG00000134982
hgnc_id : HGNC:583
consequence_terms : ['downstream_gene_variant']
protein_position : N/A
transcript_name : N/A
---
transcript_id : ENST00000507379
gene_symbol : APC
gene_id : ENSG00000134982
hgnc_id : HGNC:583
consequence_terms : ['downstream_gene_variant']
protein_position : N/A
transcript_name : N/A
---
transcript_id : ENST00000508376
gene_symbol : APC
gene_id : ENSG00000134982
hgnc_id : HGNC:583
amino_acids : EKI/DX
consequence_terms : ['frameshift_variant']
protein_position : 1309-1311
transcript_name : EKI1309-1311DX
---
transcript_id : ENST00000508624
gene_symbol : APC
gene_id : ENSG00000134982
hgnc_id : HGNC:583
consequence_terms : ['3_prime_UTR_variant', 'NMD_transcript_variant']
protein_position : N/A
transcript_name : N/A
---
transcript_id : ENST00000512211
gene_symbol : APC
gene_id : ENSG00000134982
hgnc_id : HGNC:583
consequence_terms : ['downstream_gene_variant']
protein_position : N/A
transcript_name : N/A
---
transcript_id : ENST00000520401
gene_id : ENSG00000258864
consequence_terms : ['intron_variant', 'NMD_transcript_variant']
protein_position : N/A
transcript_name : N/A
---
1 maintainer
Metadata
1 maintainer
Release files for bioinfo-toolset 1.4
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Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| bioinfo_toolset-1.4.tar.gz | 11.1 kB | Without provenance | Details for bioinfo_toolset-1.4.tar.gz |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Actions Reset |
|---|---|---|---|---|
| bioinfo_toolset-1.4-py3-none-any.whl | Python 3 | none | any | Details for bioinfo_toolset-1.4-py3-none-any.whl |
Total release size: 24.2 kB
Release files / bioinfo_toolset-1.4.tar.gz
| Download URL | bioinfo_toolset-1.4.tar.gz |
|---|---|
| Size | 11.1 kB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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twine/3.4.1 importlib_metadata/4.6.0 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.61.1 CPython/3.9.7
|
Release files / bioinfo_toolset-1.4-py3-none-any.whl
| Download URL | bioinfo_toolset-1.4-py3-none-any.whl |
|---|---|
| Size | 13.1 kB |
| Tags | Python 3 |
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twine/3.4.1 importlib_metadata/4.6.0 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.61.1 CPython/3.9.7
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