Comments (5)
Instead of an add_strand function, would a generic extend_bed function that allows you to extend the bed object you currently and populate these fields with . and then allow you to use the each function to add corresponding values?
from pybedtools.
If I understand correctly, you mean something like:
def extend_fields(feature, n):
fields = feature.fields[:]
while len(fields) < n:
fields.append('.')
return pybedtools.create_interval_from_list(fields)
Then you can write a user-defined function that assumes the fields have been padded:
def add_strand(feature, strand):
feature[5] = strand
return feature
So you would use them like this:
import pybedtools
x = pybedtools.example_bedtool('venn.b.bed')
y = x.each(extend_fields, 6).each(add_strand, '+').saveas()
I think that works pretty well. It leaves the manipulation of the number of fields (BED, GFF, VCF) up to the user, which I would prefer since it maintains flexibility. I'll add this to pybedtools.featurefuncs
in Cython so it's hopefully faster.
from pybedtools.
That exactly what I was getting at. Sorry for not being very clear. I would also change the name from add_feature to update feature at that point, since the field would already exist.
from pybedtools.
OK, I added extend_fields
in 5cc273b -- thanks for the suggestion.
Rather than make separate functions for every possible operation, I'd prefer to leave it up to the user to create the functions they want . . . so in this case update_strand
would be up to you to write/name.
from pybedtools.
Sounds great. Ya makes more sense for a user to make and name their own functions. Thanks for adding the functionality.
from pybedtools.
Related Issues (20)
- Support Python 3.10 and 3.11 HOT 1
- "python setup.py bdist_wheel did not run successfully" when pip installing with python v3.11 HOT 8
- to_dataframe() creates 0th row with generic names in nucleotide_content HOT 2
- build failure under python 3.11 HOT 6
- pybedtools intersect error HOT 2
- Cannot create a BedTool object from list of regions that uses np.int64 coordinates
- remove historical py27 support HOT 1
- bedtools intersect reported incorrect interval intersection HOT 3
- Cythonizing files requires `language_level=2` to be set in cythonize() HOT 4
- pybedtools multi_bam_coverage assistance HOT 2
- "fastaFromBed" error HOT 2
- intersect with multiple -b arguments not working with -sorted HOT 1
- Unable to install pybedtools==0.9.1 in Python3.10 HOT 4
- Len modifying the Bedtools after a filter HOT 2
- Has pybedtools considered packaging bedtools? HOT 3
- how to mask gap regions for randomization? HOT 1
- Issue while doing pip install pybedtools HOT 3
- Inconsistent behaviour when using files from `pathlib.PosixPath` with BedTool functions...
- pybedtools.bedtool.Bedtool.sort()
- total_coverage giving a incorrect value
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from pybedtools.