Seq | python utilities for manipulation of biological sequences | Genomics library
kandi X-RAY | Seq Summary
kandi X-RAY | Seq Summary
(abandoned) python utilities for manipulation of biological sequences
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Top functions reviewed by kandi - BETA
- Deprecated use create_taxonomy_db
- Create NCBI taxonomy database
- Make the merged db
- Make the names table
- Create nodes for nodes
- Download data from NCBI
- Write a sequence of sequences to a FASTA file
- Convert sequence to Phylip
- Rename the sequence
- Read a list of sequences from a string
- Convert record to dictionary
- Create the names table
- Check if a row is a primary name
- Raise a SystemError if sys version is greater than min
- Search a list of directories
- Makes a reverse translation dictionary
- Determines the operating system type
- List duplicates
- Read species taxonomy
- Read taxonomy data
- Read a dmp file
- Create nodes table
- Get the version of the initfile
Seq Key Features
Seq Examples and Code Snippets
def is_nested(seq):
"""Returns true if its input is a nested structure.
Refer to [tf.nest](https://www.tensorflow.org/api_docs/python/tf/nest)
for the definition of a nested structure.
Args:
seq: the value to test.
Returns:
True
static void subseq(String p, String up) {
if (up.isEmpty()) {
System.out.println(p);
return;
}
char ch = up.charAt(0);
subseq(p + ch, up.substring(1));
subseq(p, up.substring(1));
}
Community Discussions
Trending Discussions on Seq
QUESTION
I'm wondering what the idiomatic way in Scala would be to convert a Seq
of Option[A]
to an Option[Seq[A]]
, where the result is None
if any of the input options were None
.
ANSWER
Answered 2021-Jun-15 at 18:17The idiomatic way is probably to use what is generally called traverse
.
I'd recommend reading Cats' documentation about it: https://typelevel.org/cats/typeclasses/traverse.html
With Cats, it would be as easy as:
QUESTION
I made one graph with 'two line' y-axis title using the code ylab(expression(paste()
ANSWER
Answered 2021-Jun-15 at 13:56One way would be to adjust the margins giving more space to the left.
QUESTION
This example has been tested with Spark 2.4.x. Let's consider 2 simple dataframes:
...ANSWER
Answered 2021-Jun-15 at 12:49This seems like a bug introduced by a bug fix in this ticket. The result was wrong for outer joins
.
Hence the need to add a Project
node (packing of the struct) before the Join
node.
However, we end up with this kind of query plan:
QUESTION
When running the first "almost MWE" code immediately below, which uses conditional panels and a "renderUI" function in the server section, it only runs correctly when I comment out the 3rd line from the bottom, observeEvent(vector.final(periods(),yield_input()),{yield_vector.R <<- unique(vector.final(periods(),yield_input()))})
. If I run the code with this line activated, it crashes and I get the error message Error in [: subscript out of bounds
which per my research means it is trying to access an array out of its boundary.
ANSWER
Answered 2021-Jun-14 at 22:51Replace the line you commented out with this
QUESTION
The example data looks like this:
...ANSWER
Answered 2021-Jun-14 at 17:24We can assign. Here, we used lapply
to loop over the columns (in case there are some difference in type
, then lapply
preserves it while apply
converts to matrix
and there would be a single type for those)
QUESTION
Julia Code:
...ANSWER
Answered 2021-Jun-14 at 17:00Use:
QUESTION
Edit: It looks like this is a known issue with the "cascade" method. Results that return NA values after the first attempt don't like being converted to doubles when subsequent methods return lat/lons.
Data: I have a list of addresses that I need to geocode. I'm using lapply()
to split-apply-combine, which works, but very slowly. My thought to split (further)-apply-combine is returning errors about dim names and sizes that are confusing to me.
ANSWER
Answered 2021-Jun-14 at 15:59It is working with dplyr
1.0.6
QUESTION
I have a set of data
...ANSWER
Answered 2021-Jun-14 at 16:20Just multiply with NA
as any operation with NA
results in NA
and here we could either multiply or add (+
) or subtract (-
) or divide (/
) and it still returns NA
QUESTION
I am trying to write a unit test code for my Spark-Scala notebook using scalatest.funsuite but the notebook with test() is not getting executed in databricks. Could you please let me know how can I run it?
Here is the sample test code for the same.
...ANSWER
Answered 2021-Jun-14 at 15:42You need to explicitly create the object for that test suite & execute it. In IDE you're relying on specific runner, but it doesn't work in the notebook environment.
You can use either the .execute
function of create object (docs):
QUESTION
I have a DB in MongoDB
like this:
ANSWER
Answered 2021-Jun-14 at 15:39$filter
to iterate loop ofSeries
array$regexMatch
to search format inseb
$size
to get total elements in filtered result
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install Seq
You can use Seq like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
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