lineage | genetic genealogy and the analysis of consumer DNA test | Genomics library
kandi X-RAY | lineage Summary
kandi X-RAY | lineage Summary
tools for genetic genealogy and the analysis of consumer DNA test results
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Top functions reviewed by kandi - BETA
- Return a dict of command - line arguments
- Build a ConfigParser from a root directory
- Get the project root directory
- Extract version information from VCS
- Create a versioneer config file
- Install versioneer
- Scans the given setup py py py
lineage Key Features
lineage Examples and Code Snippets
df_up = pd.merge(sample_data, upstream_data, left_on = ['From Country', 'From Town','FromStreet'], right_on = ['ToCountry', 'ToTown',
'ToStreet'], how = 'left', suffixes= ('_current', ''))[['AttributeName','Lineage Step','From Count
df.groupby(['uniprot_id','protein_name'])[['protein_family','protein_subfamily']].agg('; '.join(x))
df.sort_values(['protein_family','protein_subfamily']).groupby(...)
df.groupby(['uniprot_
out = (sample_data.groupby('AttributeName')
.apply(lambda x: x[~x['From Country'].isin(x['ToCountry'])])
)
AttributeName Lineage Step From Country From Town FromStreet ToCountry To
(pd.DataFrame({'ID': df['ID'],
'Email': df.select_dtypes(object)
.applymap(lambda x: bool(re.findall('\S+@\S+', str(x))))
.any(axis=1),
'Phone': df.select_dt
def create_dicts(filename):
'''Transforms the unique_taxids_lineage_allsamples file into a dictionary.
Note: There can be multiple ids mapping to the same lineage info. Therefore ids should be values.'''
# Creating a genus_dict
myfasta = {}
if myfasta[sequence]:
myfasta[sequence].append(lineage_id)
else:
myfasta[sequence] = [lineage_id]
def find_lineage(cell_nb, full_ancestry):
ancestry = []
while cell_nb:
cell_nb = full_ancestry[cell_nb - 1]['mother_nb']
ancestry.append(cell_nb)
return ancestry
print(find_lineage(13, full_ancestry))
for i in range(1, 11):
for t in range(1, 11):
print(f"{i*t:>5}", end="")
print()
1 2 3 4 5 6 7 8 9 10
2 4 6 8 10 12 14 16 18 20
3 6 9 12
datalake_spark_dataframe_new=datalake_spark_dataframe
datalake_spark_dataframe.write.mode("overwrite").option("header", "true").format("parquet").save("abfss://")
for i in range(287):
print(i)
datalake_spark_dataframe_new=spark.read.pa
def get_lineage_translator(self, taxids):
"""Given a valid taxid number, return its corresponding lineage track as a
hierarchically sorted list of parent taxids.
# relevant section from ncbi tax
Community Discussions
Trending Discussions on lineage
QUESTION
I have a terraform state file (json) with some deprecated attributes.
I would like to remove theses deprecated attributes.
I try to use jq
and select()
&& del()
but did not succeed to get back my full json without the deprecated attribue timeouts.
How to get my full json without the attribute timeouts
for only one type of resources google_dns_record_set
.
ANSWER
Answered 2022-Mar-10 at 17:51Pull the del
command up front to include the whole selection as its own filter
QUESTION
I am trying to build Lineage 19.0 on a VPS running Fedora 34 Workstation. It has 8GB RAM and 20GB Swap. It is virtualized in KVM.
It had done all the other work correctly and I have doubled-check if I am leaving out on any dependencies. I had also recloned the hardware/ril path using https://github.com/LineageOS/android_hardware_ril/tree/lineage-19.0/ but it also didn't work.
This is the error.
...ANSWER
Answered 2022-Mar-10 at 16:22Found an answer:
First, ensure if you have a Samsung device that you have the latest Samsung hardware files.
Secondly, just throw in ALLOW_MISSING_DEPENDENCIES=true
in your BoardConfig.mk
QUESTION
I have a One Plus 6T. When I got it 1 year ago, I flashed the newest firmware from the official One Plus page (https://www.oneplus.com/de/support/softwareupgrade/) via fastboot in both slots and then installed LinageOS 17.1 for fajita. Now 18.1 is available since some time and I wanted to upgrade. The official page suggests using adb side load (https://wiki.lineageos.org/devices/fajita/upgrade) When going through the steps I noticed two symptoms:
- USB-File transfer is not possible.
- ADB does not recognize my device when it is in file transfer mode (it does work for USB-Tethering, MIDI and PTP)
I also see sideload failing:
...ANSWER
Answered 2021-Oct-18 at 17:57Somehow my OnePlus was recognized by another huawei driver. Uninstalling this driver through the device manager solved the issue.
QUESTION
I am using Azure Blob to store my state. I follow these [steps] (https://github.com/hashicorp/terraform-cdk/blob/main/docs/working-with-cdk-for-terraform/remote-backend.md#migrating-local-state-storage-to-remote) the only difference is that I am using the AzurermBackend. The problem is when I do terraform init
it does not migrate the existing state to the blob, it just create a new one in which there is no resources, so when i execute cdktf diff
terraform says that it needs to create each resource that was already created in the local state. I checked the file the file is empty. I also tried with thr stack.addOveride
that don't works too. Next thing I did is I execute the TF_LOG=DEBUG terraform init
and got the following logs:
ANSWER
Answered 2022-Feb-27 at 12:57You also need to specify a backend provider under main terraform config. If you don't specify it it will assume local so no migration. Something like this
QUESTION
I have the problem that in our Snowflake DWH views were built on of top views (& again on top of views). If am now trying to change the underlying table the first view is derived from, I am afraid to break things.
Heres an example:
We have a table with REGISTRATIONS
for several countries. Based on that table a view is created only showing data from US (REGISTRATIONS_US
). This view is being used to built a view containing US data from lets say 2021 (REGISTRATIONS_US_2021
). This view is again being used to build a view containing data from US in 2021 for a specific month, lets say July (REGISTRATIONS_US_202106
). It can also happen that a view is used to generate more than one view (see for example REGISTRATIONS_US_NYC
in the table provided below).
If I would now change the registrations table all the related views are affected. Therefore I need to find out how the views are related.
The only information I have is the one available in INFORMATION_SCHEMA
:
SELECT * FROM REGISTRATIONS WHERE market = 'US' REGISTRATIONS_US_2021 CREATE VIEW REGISTRATIONS_US_2021 AS
SELECT * FROM REGISTRATIONS_US WHERE year = 2021 REGISTRATIONS_US_202106 CREATE VIEW REGISTRATIONS_US_202106 AS
SELECT * FROM REGISTRATIONS_US_2021 WHERE month_id = '202106' REGISTRATIONS_US_NYC CREATE VIEW REGISTRATIONS_US_NYC AS
SELECT * FROM REGISTRATIONS_US WHERE city = 'NYC'
I would like to gain the following solution:
LINEAGE REGISTRATIONS_US > REGISTRATIONS_US_NYC REGISTRATIONS_US > REGISTRATIONS_US_2021 > REGISTRATIONS_US_202106I guess that should be somehow possible using a recursive CTE. But I just cannot imagine how since most examples of recursive CTEs to be found on Google already show the hierarchy in the table based on ids (typical manager/ employee example).
I hope my question is clear & someone can help.
...ANSWER
Answered 2022-Feb-13 at 16:15GET_OBJECT_REFERENCES could be used to track dependencies between objects:
Returns a list of objects that a specified object references. Input is currently limited to the name of a view.
QUESTION
I am trying to better understand BigQuery queryPlan, and try to establish data lineage at a column-level using that queryPlan.
Everything started fine, READ
, COMPUTE
, etc... are pretty understandable, then I crossed a JOIN
step. Using a simple query that will join two tables on a single column, and output columns from both tables:
ANSWER
Answered 2022-Feb-10 at 14:08Its not possible by the query plan. The $variables
sent to the last step TO __stage00_output
contains the column data to be sent to the output. If it is repeated, it will not be sent multiple times. It will just be showed multiple times in the final output (as there no meaning to pass same information multiple times from one step to another.)
if there is no repeated columns, it can be considered a representation of output schema, but better not use it. The query plan is meant to be used to troubleshooting and identify bottlenecks on the queries by monitoring its execution time ans so on..
QUESTION
I've Two workflowTemplates generate-output
, lib-read-outputs
and One workflow output-paramter
as follows
generate-output.yaml
ANSWER
Answered 2022-Jan-31 at 17:50DAG and steps templates do not automatically produce their child templates' outputs, even if there is only one child template.
For example, the no-parameters
template here does not produce an output, even though it invokes a template which does have an output.
QUESTION
I have a dataframe that shows lineage (in the sample data provided it is a person's route). I have another dataframe that gives me preceding information about the routes, which should slot in the same format.
First sample looks like this:
...ANSWER
Answered 2022-Jan-19 at 13:20Your first idea is doable (and seems to be the best approach).
First we merge and select the 'new' columns that we want. We also set 'Lineage Step to 0 as we will sort later:
QUESTION
I have this dataframe in python df
ANSWER
Answered 2022-Jan-11 at 23:57something like this :
QUESTION
I want to create a parquet table with certain types of fields:
name_process: String id_session: Int time_write: LocalDate or Timestamp key: String value: String
name_process id_session time_write key value OtherClass jsdfsadfsf 43434883477 schema0.table0.csv Success OtherClass jksdfkjhka 23212123323 schema1.table1.csv Success OtherClass alskdfksjd 23343212234 schema2.table2.csv Failure ExternalClass sdfjkhsdfd 34455453434 schema3.table3.csv SuccessI want to write such a table correctly. With the correct data types. Then I'm going to read the partitions from it. I'm trying to implement read and write. But it turns out badly so far.
...ANSWER
Answered 2021-Dec-16 at 12:49Problem
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Install lineage
You can use lineage 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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