lineage | genetic genealogy and the analysis of consumer DNA test | Genomics library

 by   apriha Python Version: 4.4.0 License: MIT

kandi X-RAY | lineage Summary

kandi X-RAY | lineage Summary

lineage is a Python library typically used in Artificial Intelligence, Genomics applications. lineage has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can install using 'pip install lineage' or download it from GitHub, PyPI.

tools for genetic genealogy and the analysis of consumer DNA test results
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            kandi-support Support

              lineage has a low active ecosystem.
              It has 117 star(s) with 22 fork(s). There are 9 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 7 open issues and 36 have been closed. On average issues are closed in 470 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of lineage is 4.4.0

            kandi-Quality Quality

              lineage has 0 bugs and 0 code smells.

            kandi-Security Security

              lineage has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              lineage code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              lineage is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              lineage releases are available to install and integrate.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              It has 3696 lines of code, 174 functions and 12 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed lineage and discovered the below as its top functions. This is intended to give you an instant insight into lineage implemented functionality, and help decide if they suit your requirements.
            • 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
            Get all kandi verified functions for this library.

            lineage Key Features

            No Key Features are available at this moment for lineage.

            lineage Examples and Code Snippets

            How to merge data vertically so there are multiple lines instead of multiple columns
            Pythondot img1Lines of Code : 25dot img1License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            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
            Combining Duplicate rows in pandas dataframe
            Pythondot img2Lines of Code : 6dot img2License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            df.groupby(['uniprot_id','protein_name'])[['protein_family','protein_subfamily']].agg('; '.join(x))
            
            df.sort_values(['protein_family','protein_subfamily']).groupby(...)
            
            df.groupby(['uniprot_
            Using the isin() function on grouped data
            Pythondot img3Lines of Code : 9dot img3License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            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
            Check entire pandas data frame for emails and phone numbers
            Pythondot img4Lines of Code : 18dot img4License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            (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
            Why are the values in my dictionary returning as a list within a list for each element?
            Pythondot img5Lines of Code : 23dot img5License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            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
            How to remove duplicates from fasta file but keep at least one per group based on header
            Pythondot img6Lines of Code : 6dot img6License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            myfasta = {}
            if myfasta[sequence]:
                myfasta[sequence].append(lineage_id)
            else:
                myfasta[sequence] = [lineage_id]
            
            Writing a function to Trace bacterial lineage in python
            Pythondot img7Lines of Code : 26dot img7License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            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))
            
            How do I make a good multiplication chart
            Pythondot img8Lines of Code : 16dot img8License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            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  
            applying cache() and count() to Spark Dataframe in Databricks is very slow [pyspark]
            Pythondot img9Lines of Code : 15dot img9License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
            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
            ete3 error : could not be translated into taxids! - Bioinformatics
            Pythondot img10Lines of Code : 8dot img10License : Strong Copyleft (CC BY-SA 4.0)
            copy iconCopy
                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

            QUESTION

            select and delete attributes with JQ
            Asked 2022-Mar-10 at 17:51
            Info

            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.

            Problem

            How to get my full json without the attribute timeouts for only one type of resources google_dns_record_set.

            Data ...

            ANSWER

            Answered 2022-Mar-10 at 17:51

            Pull the del command up front to include the whole selection as its own filter

            Source https://stackoverflow.com/questions/71428557

            QUESTION

            error: "libreference-ril (SHARED_LIBRARIES android-arm) missing libril (SHARED_LIBRARIES android-arm)" while building Lineage19
            Asked 2022-Mar-10 at 16:22

            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 16:22

            Found 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

            Source https://stackoverflow.com/questions/71427226

            QUESTION

            USB-file-transfer and adb sideload not working
            Asked 2022-Mar-01 at 13:12

            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:

            1. USB-File transfer is not possible.
            2. 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 17:57

            Somehow my OnePlus was recognized by another huawei driver. Uninstalling this driver through the device manager solved the issue.

            Source https://stackoverflow.com/questions/68795115

            QUESTION

            Local TFstate does not migrate to remote location (Azure Blob)
            Asked 2022-Feb-27 at 12:57

            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 12:57

            You 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

            Source https://stackoverflow.com/questions/70424811

            QUESTION

            Table Lineage with Recursive CTE using view definition in information schema
            Asked 2022-Feb-13 at 16:15

            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:

            TABLE_NAME VIEW_DEFINITION REGISTRATIONS_US CREATE VIEW REGISTRATIONS_US AS
            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_202106

            I 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 16:15

            GET_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.

            Source https://stackoverflow.com/questions/70263637

            QUESTION

            Bigquery query plan produce unknown output
            Asked 2022-Feb-10 at 14:08

            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 14:08

            Its 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..

            Source https://stackoverflow.com/questions/71062753

            QUESTION

            Unable to pass output parameters from one workflowTemplate to a workflow via another workflowTemplate
            Asked 2022-Jan-31 at 17:50

            I've Two workflowTemplates generate-output, lib-read-outputs and One workflow output-paramter as follows

            1. generate-output.yaml
            ...

            ANSWER

            Answered 2022-Jan-31 at 17:50
            DAG and steps templates don't produce outputs by default

            DAG 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.

            Source https://stackoverflow.com/questions/70897648

            QUESTION

            How to merge data vertically so there are multiple lines instead of multiple columns
            Asked 2022-Jan-19 at 13:27

            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 13:20

            Your 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:

            Source https://stackoverflow.com/questions/70770026

            QUESTION

            Combining Duplicate rows in pandas dataframe
            Asked 2022-Jan-11 at 23:57

            I have this dataframe in python df

            ...

            ANSWER

            Answered 2022-Jan-11 at 23:57

            QUESTION

            How create parquet table in scala?
            Asked 2021-Dec-16 at 12:49

            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 Success

            I 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 12:49

            Problem

            When you do this

            Source https://stackoverflow.com/questions/70378626

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install lineage

            You can install using 'pip install lineage' or download it from GitHub, PyPI.
            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.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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            Install
          • PyPI

            pip install lineage

          • CLONE
          • HTTPS

            https://github.com/apriha/lineage.git

          • CLI

            gh repo clone apriha/lineage

          • sshUrl

            git@github.com:apriha/lineage.git

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