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StORF-Reporter-0.5.57
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مشاهده بیشترتوضیحات
StORF-Reporter - A tool that takes as input an annotated genome and returns missed CDS genes from the unannotated regions.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | OS Independent |
| نام فایل | StORF-Reporter-0.5.57 |
| نام | StORF-Reporter |
| نسخه کتابخانه | 0.5.57 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Nicholas Dimonaco |
| ایمیل نویسنده | nicholas@dimonaco.co.uk |
| آدرس صفحه اصلی | https://github.com/NickJD/StORF-Reporter |
| آدرس اینترنتی | https://pypi.org/project/StORF-Reporter/ |
| مجوز | - |
# StORF-Reporter - Preprint: https://www.biorxiv.org/content/10.1101/2022.03.31.486628v3
### StORF-Reporter, a toolkit that takes as input an annotated genome and returns missed CDS genes from the Unannotated Regions (URs).
# Please use `pip3 install StORF-Reporter' to install StORF-Reporter.
### This will also install numpy and the 'ORForise' package from https://github.com/NickJD/ORForise to allow for additional functionality.
### Consider using '--no-cache-dir' with pip to ensure the download of the newest version of the package.
## Please Note: To report Con-StORFs (Pseudogenes and genes that reuse stop codons), use "-con_storfs True" and "-con_only" to disable reporting of StORFs (missed complete genes).
#############################################################
# UR-Extractor
### Subpackage to extract Unannotated Regions from DNA sequences using FASTA and GFF files as input.
### Menu - (UR-Extractor -h):
```console
UR-Extractor -f genomes/E-coli.fasta.gz -gff genomes/E-coli.gff -o genomes/E-coli_UR -gz True
```
```python
usage: UR-Extractor [-h] -f FASTA -gff GFF [-ident IDENT] [-min_len MINLEN]
[-max_len MAXLEN] [-ex_len EXLEN]
[-gene_ident GENE_IDENT] [-o OUT_FILE]
[-gz {True,False}] [-v {True,False}]
StORF-Reporter v0.5.56: UR-Extractor Run Parameters.
optional arguments:
-h, --help show this help message and exit
-f FASTA, --fasta_seq FASTA
FASTA file for Unannotated Region seq extraction
-gff GFF GFF annotation file for the FASTA
-ident IDENT Identifier given for Unannotated Region output
sequences: Default "Input"_UR
-min_len MINLEN Minimum UR Length: Default 30
-max_len MAXLEN Maximum UR Length: Default 100,000
-ex_len EXLEN UR Extension Length: Default 50
-gene_ident GENE_IDENT
Identifier used for extraction of "unannotated"
regions "CDS,rRNA,tRNA": Default for Ensembl_Bacteria
= "ID=gene"
-o OUT_FILE, --output_file OUT_FILE
Output file - Without filetype - default appends "_UR"
to end of input gff filename (replaces '.gff')
-gz {True,False} Default - False: Output as .gz
-v {True,False} Default - False: Print out runtime status
```
## StORF-Finder
### Subpackage to extract Stop - Stop Codon (St)ORFs from Fasta sequences - Worked directly with the output of UR-Extractor.
### Menu - (StORF-Finder -h):
```console
StORF-Finder -seq genomes/E-coli_UR.fasta.gz -o genomes/E-coli_UR_StORF -gz True
```
```python
usage: StORF-Finder [-h] -f FASTA [-ua {True,False}] [-wc {True,False}]
[-ps {True,False}] [-filt [{none,soft,hard}]]
[-aa {True,False}] [-aa_only {True,False}]
[-con_storfs {True,False}] [-con_only {True,False}]
[-stop_ident {True,False}] [-type [{StORF,CDS,ORF}]]
[-minorf MIN_ORF] [-maxorf MAX_ORF]
[-codons STOP_CODONS] [-olap OVERLAP_NT]
[-gff {True,False}] [-s SUFFIX]
[-so [{start_pos,strand}]] [-spos {True,False}]
[-o OUT_FILE] [-af AFFIX] [-lw {True,False}]
[-gz {True,False}] [-v {True,False}]
StORF-Reporter v0.5.56: StORF-Finder Run Parameters.
optional arguments:
-h, --help show this help message and exit
-f FASTA Input FASTA File
-ua {True,False} Default - Treat input as Unannotated: Use "-ua False"
for standard fasta
-wc {True,False} Default - False: StORFs reported across entire
sequence
-ps {True,False} Default - False: Partial StORFs reported
-filt [{none,soft,hard}]
Default - "hard": Filtering level "none" is not
recommended, "soft" for single strand filtering and
hard for both-strand longest-first tiling
-aa {True,False} Default - False: Report StORFs as amino acid sequences
-aa_only {True,False}
Default - False: Only output Amino Acid Fasta
-con_storfs {True,False}
Default - False: Output Consecutive StORFs
-con_only {True,False}
Default - False: Only output Consecutive StORFs
-stop_ident {True,False}
Default - True: Identify Stop Codon positions with '*'
-type [{StORF,CDS,ORF}]
Default - "StORF": Which GFF feature type for StORFs
to be reported as in GFF
-minorf MIN_ORF Default - 100: Minimum StORF size in nt
-maxorf MAX_ORF Default - 50kb: Maximum StORF size in nt
-codons STOP_CODONS Default - ('TAG,TGA,TAA'): List Stop Codons to use
-olap OVERLAP_NT Default - 50: Maximum number of nt of a StORF which
can overlap another StORF.
-gff {True,False} Default - True: StORF Output a GFF file
-s SUFFIX Default - Do not append suffix to genome ID
-so [{start_pos,strand}]
Default - Start Position: How should StORFs be ordered
when >1 reported in a single UR.
-spos {True,False} Default - False: Print out StORF positions inclusive
of first stop codon
-o OUT_FILE Default - False: Without filetype - default appends
'_StORF-R' to end of input gff filename (replaces
'.gff')
-af AFFIX Default - None: '-af Con-StORFs' can be used to append
an identifier to output filename to distinguish Con-
StORF from StORF runs)
-lw {True,False} Default - True: Line wrap FASTA sequence output at 60
chars
-gz {True,False} Default - False: Output as .gz
-v {True,False} Default - False: Print out runtime status
```
##########
## StORF-Reporter
### Subpackage to run UR-Extractor and StORF-Finder together on a PROKKA annotation and produce output which can be used in tools such as Roary that by default accepts PROKKA's output format:
#### For use on a single PROKKA output directory -
```console
StORF-Reporter -anno PROKKA -pd ../PROKKA_04062022/
```
#### For use on a directory containing multiple PROKKA output gffs
```console
StORF-Reporter -anno PROKKA -p_gff ../PROKKA_Outputs/
```
### Menu - (StORF-Reporter -h):
```python
usage: StORF-Reporter [-h] -anno [{PROKKA,Ensembl,Gene}] [-pd PROKKA_DIR]
[-p_gff PROKKA_GFFS] [-col GENOME_COLLECTION]
[-comb COMBINED_GFFS] [-spos {True,False}]
[-rs {True,False}] [-sout {True,False}]
[-con_storfs {True,False}] [-con_only {True,False}]
[-min_len MINLEN] [-max_len MAXLEN] [-ex_len EXLEN]
[-minorf MIN_ORF] [-type [{StORF,CDS,ORF}]]
[-olap OVERLAP_NT] [-ao ALLOWED_OVERLAP]
[-lw {True,False}] [-aa {True,False}]
[-gz {True,False}] [-v {True,False}]
StORF-Reporter v0.5.56: StORF-Reporter Run Parameters.
optional arguments:
-h, --help show this help message and exit
-anno [{PROKKA,Ensembl,Gene}]
Default - PROKKA: Annotation type to be StORF-
Reported:Options: PROKKA =
"misc_RNA,gene,mRNA,CDS,tRNA,tmRNA,CRISPR";Ensembl =
"ID=gene" ;Gene = "gene"
-pd PROKKA_DIR, --PROKKA_dir PROKKA_DIR
PROKKA output directory to be used if PROKKA chosen -
Produces a new GFF and FASTA containing all Coding and
Non-Coding Seqs
-p_gff PROKKA_GFFS, --PROKKA_GFFs PROKKA_GFFS
Provide directory contain GFFs to be StORFed - Only
produces modified GFFs
-col GENOME_COLLECTION
Provide directories containing a collection of
matching FASTA and GFF files(list .fa then .gff
containing directories separated by commas -
./FA,./GFF)
-comb COMBINED_GFFS Provide directory containing GFFs with sequences
combined into single file to be StORFed - Only
produces modified GFFs
-spos {True,False} Default - False: Print out StORF positions inclusive
of first stop codon
-rs {True,False} Default - True: Remove stop "*" from StORF amino acid
sequences
-sout {True,False} Default - False: Print out StORF sequences separately?
-con_storfs {True,False}
Default - False: Output Consecutive StORFs
-con_only {True,False}
Default - False: Only output Consecutive StORFs
-min_len MINLEN Default - 30: Minimum UR Length
-max_len MAXLEN Default - 100,000: Maximum UR Length
-ex_len EXLEN Default - 50: UR Extension Length
-minorf MIN_ORF Default - 100: Minimum StORF size in nt
-type [{StORF,CDS,ORF}]
Default - "CDS": Which GFF feature type for StORFs to
be reported as in GFF - "CDS" is probably needed for
use in tools such as Roary
-olap OVERLAP_NT Default - 50: Maximum number of nt of a StORF which
can overlap another StORF.
-ao ALLOWED_OVERLAP Default - 50 nt: Maximum overlap between a StORF and
an original gene.
-lw {True,False} Default - True: Line wrap FASTA sequence output at 60
chars
-aa {True,False} Default - False: Report StORFs as amino acid sequences
-gz {True,False} Default - False: Output as .gz
-v {True,False} Default - False: Print out runtime status
```
## Test Datasets:
### The direcotory 'Genomes' contains GFF and FASTA datasets to test a users installation and use of StORF-Reporter. Example output files are also available for comparison.
نیازمندی
| مقدار | نام |
|---|---|
| - | numpy |
| - | ORForise |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6 | Python |
نحوه نصب
نصب پکیج whl StORF-Reporter-0.5.57:
pip install StORF-Reporter-0.5.57.whl
نصب پکیج tar.gz StORF-Reporter-0.5.57:
pip install StORF-Reporter-0.5.57.tar.gz