Importing GFF file with Biopython











up vote
4
down vote

favorite












Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file?



For example,



from Bio import Entrez as ez
ez.email = '...'
handle = ez.efetch(db='gene', id='AE015451.2', rettype='genbank', retmode='xml')
h = handle.read()
print(h)


This will import a Gebank xml file for Pseudomonas putida. Is there a way to do this for a GFF file?










share|improve this question









New contributor




Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.




















  • Please remember to confirm an answer once you've received one.
    – Stephopolis
    2 days ago















up vote
4
down vote

favorite












Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file?



For example,



from Bio import Entrez as ez
ez.email = '...'
handle = ez.efetch(db='gene', id='AE015451.2', rettype='genbank', retmode='xml')
h = handle.read()
print(h)


This will import a Gebank xml file for Pseudomonas putida. Is there a way to do this for a GFF file?










share|improve this question









New contributor




Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.




















  • Please remember to confirm an answer once you've received one.
    – Stephopolis
    2 days ago













up vote
4
down vote

favorite









up vote
4
down vote

favorite











Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file?



For example,



from Bio import Entrez as ez
ez.email = '...'
handle = ez.efetch(db='gene', id='AE015451.2', rettype='genbank', retmode='xml')
h = handle.read()
print(h)


This will import a Gebank xml file for Pseudomonas putida. Is there a way to do this for a GFF file?










share|improve this question









New contributor




Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.











Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file?



For example,



from Bio import Entrez as ez
ez.email = '...'
handle = ez.efetch(db='gene', id='AE015451.2', rettype='genbank', retmode='xml')
h = handle.read()
print(h)


This will import a Gebank xml file for Pseudomonas putida. Is there a way to do this for a GFF file?







biopython ncbi genbank gff






share|improve this question









New contributor




Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.











share|improve this question









New contributor




Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.









share|improve this question




share|improve this question








edited 12 hours ago









Daniel Standage

1,866324




1,866324






New contributor




Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.









asked Dec 10 at 2:19









Alex Summers

233




233




New contributor




Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.





New contributor





Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.






Alex Summers is a new contributor to this site. Take care in asking for clarification, commenting, and answering.
Check out our Code of Conduct.












  • Please remember to confirm an answer once you've received one.
    – Stephopolis
    2 days ago


















  • Please remember to confirm an answer once you've received one.
    – Stephopolis
    2 days ago
















Please remember to confirm an answer once you've received one.
– Stephopolis
2 days ago




Please remember to confirm an answer once you've received one.
– Stephopolis
2 days ago










3 Answers
3






active

oldest

votes

















up vote
9
down vote



accepted










No, there is currently no GFF support in biopython.



However, you can read in GFF files into python using this package, gffutils. There are also a few other packages to read/write GFF files, like gff3.






share|improve this answer




























    up vote
    1
    down vote













    I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model.



    The only downside is that I believe it is no longer actively supported. It is however the package that the BioPython docs use generally. There are plans to properly incorporate GFF/GTF parsers in to BP in the not too distant future according to that link though.






    share|improve this answer




























      up vote
      0
      down vote













      Most GFF parsers handle the work of reading annotation data into objects for convenient data access, but most do not handle the important task of resolving relationships between features. The tag Python library does both, grouping related features together for inspection, traversal, and feature-by-feature processing.



      CAVEAT: The tag library only supports GFF3.



      DISCLAIMER: I'm the developer of the tag library, so this is a shameless plug. :-)






      share|improve this answer





















        Your Answer





        StackExchange.ifUsing("editor", function () {
        return StackExchange.using("mathjaxEditing", function () {
        StackExchange.MarkdownEditor.creationCallbacks.add(function (editor, postfix) {
        StackExchange.mathjaxEditing.prepareWmdForMathJax(editor, postfix, [["$", "$"], ["\\(","\\)"]]);
        });
        });
        }, "mathjax-editing");

        StackExchange.ready(function() {
        var channelOptions = {
        tags: "".split(" "),
        id: "676"
        };
        initTagRenderer("".split(" "), "".split(" "), channelOptions);

        StackExchange.using("externalEditor", function() {
        // Have to fire editor after snippets, if snippets enabled
        if (StackExchange.settings.snippets.snippetsEnabled) {
        StackExchange.using("snippets", function() {
        createEditor();
        });
        }
        else {
        createEditor();
        }
        });

        function createEditor() {
        StackExchange.prepareEditor({
        heartbeatType: 'answer',
        convertImagesToLinks: false,
        noModals: true,
        showLowRepImageUploadWarning: true,
        reputationToPostImages: null,
        bindNavPrevention: true,
        postfix: "",
        imageUploader: {
        brandingHtml: "Powered by u003ca class="icon-imgur-white" href="https://imgur.com/"u003eu003c/au003e",
        contentPolicyHtml: "User contributions licensed under u003ca href="https://creativecommons.org/licenses/by-sa/3.0/"u003ecc by-sa 3.0 with attribution requiredu003c/au003e u003ca href="https://stackoverflow.com/legal/content-policy"u003e(content policy)u003c/au003e",
        allowUrls: true
        },
        onDemand: true,
        discardSelector: ".discard-answer"
        ,immediatelyShowMarkdownHelp:true
        });


        }
        });






        Alex Summers is a new contributor. Be nice, and check out our Code of Conduct.










        draft saved

        draft discarded


















        StackExchange.ready(
        function () {
        StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fbioinformatics.stackexchange.com%2fquestions%2f5616%2fimporting-gff-file-with-biopython%23new-answer', 'question_page');
        }
        );

        Post as a guest















        Required, but never shown

























        3 Answers
        3






        active

        oldest

        votes








        3 Answers
        3






        active

        oldest

        votes









        active

        oldest

        votes






        active

        oldest

        votes








        up vote
        9
        down vote



        accepted










        No, there is currently no GFF support in biopython.



        However, you can read in GFF files into python using this package, gffutils. There are also a few other packages to read/write GFF files, like gff3.






        share|improve this answer

























          up vote
          9
          down vote



          accepted










          No, there is currently no GFF support in biopython.



          However, you can read in GFF files into python using this package, gffutils. There are also a few other packages to read/write GFF files, like gff3.






          share|improve this answer























            up vote
            9
            down vote



            accepted







            up vote
            9
            down vote



            accepted






            No, there is currently no GFF support in biopython.



            However, you can read in GFF files into python using this package, gffutils. There are also a few other packages to read/write GFF files, like gff3.






            share|improve this answer












            No, there is currently no GFF support in biopython.



            However, you can read in GFF files into python using this package, gffutils. There are also a few other packages to read/write GFF files, like gff3.







            share|improve this answer












            share|improve this answer



            share|improve this answer










            answered Dec 10 at 2:57









            conchoecia

            1,397123




            1,397123






















                up vote
                1
                down vote













                I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model.



                The only downside is that I believe it is no longer actively supported. It is however the package that the BioPython docs use generally. There are plans to properly incorporate GFF/GTF parsers in to BP in the not too distant future according to that link though.






                share|improve this answer

























                  up vote
                  1
                  down vote













                  I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model.



                  The only downside is that I believe it is no longer actively supported. It is however the package that the BioPython docs use generally. There are plans to properly incorporate GFF/GTF parsers in to BP in the not too distant future according to that link though.






                  share|improve this answer























                    up vote
                    1
                    down vote










                    up vote
                    1
                    down vote









                    I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model.



                    The only downside is that I believe it is no longer actively supported. It is however the package that the BioPython docs use generally. There are plans to properly incorporate GFF/GTF parsers in to BP in the not too distant future according to that link though.






                    share|improve this answer












                    I would use BCBio for gff handling as it is written to directly interface with BioPython’s object model.



                    The only downside is that I believe it is no longer actively supported. It is however the package that the BioPython docs use generally. There are plans to properly incorporate GFF/GTF parsers in to BP in the not too distant future according to that link though.







                    share|improve this answer












                    share|improve this answer



                    share|improve this answer










                    answered 2 days ago









                    Joe Healey

                    29516




                    29516






















                        up vote
                        0
                        down vote













                        Most GFF parsers handle the work of reading annotation data into objects for convenient data access, but most do not handle the important task of resolving relationships between features. The tag Python library does both, grouping related features together for inspection, traversal, and feature-by-feature processing.



                        CAVEAT: The tag library only supports GFF3.



                        DISCLAIMER: I'm the developer of the tag library, so this is a shameless plug. :-)






                        share|improve this answer

























                          up vote
                          0
                          down vote













                          Most GFF parsers handle the work of reading annotation data into objects for convenient data access, but most do not handle the important task of resolving relationships between features. The tag Python library does both, grouping related features together for inspection, traversal, and feature-by-feature processing.



                          CAVEAT: The tag library only supports GFF3.



                          DISCLAIMER: I'm the developer of the tag library, so this is a shameless plug. :-)






                          share|improve this answer























                            up vote
                            0
                            down vote










                            up vote
                            0
                            down vote









                            Most GFF parsers handle the work of reading annotation data into objects for convenient data access, but most do not handle the important task of resolving relationships between features. The tag Python library does both, grouping related features together for inspection, traversal, and feature-by-feature processing.



                            CAVEAT: The tag library only supports GFF3.



                            DISCLAIMER: I'm the developer of the tag library, so this is a shameless plug. :-)






                            share|improve this answer












                            Most GFF parsers handle the work of reading annotation data into objects for convenient data access, but most do not handle the important task of resolving relationships between features. The tag Python library does both, grouping related features together for inspection, traversal, and feature-by-feature processing.



                            CAVEAT: The tag library only supports GFF3.



                            DISCLAIMER: I'm the developer of the tag library, so this is a shameless plug. :-)







                            share|improve this answer












                            share|improve this answer



                            share|improve this answer










                            answered 12 hours ago









                            Daniel Standage

                            1,866324




                            1,866324






















                                Alex Summers is a new contributor. Be nice, and check out our Code of Conduct.










                                draft saved

                                draft discarded


















                                Alex Summers is a new contributor. Be nice, and check out our Code of Conduct.













                                Alex Summers is a new contributor. Be nice, and check out our Code of Conduct.












                                Alex Summers is a new contributor. Be nice, and check out our Code of Conduct.
















                                Thanks for contributing an answer to Bioinformatics Stack Exchange!


                                • Please be sure to answer the question. Provide details and share your research!

                                But avoid



                                • Asking for help, clarification, or responding to other answers.

                                • Making statements based on opinion; back them up with references or personal experience.


                                Use MathJax to format equations. MathJax reference.


                                To learn more, see our tips on writing great answers.





                                Some of your past answers have not been well-received, and you're in danger of being blocked from answering.


                                Please pay close attention to the following guidance:


                                • Please be sure to answer the question. Provide details and share your research!

                                But avoid



                                • Asking for help, clarification, or responding to other answers.

                                • Making statements based on opinion; back them up with references or personal experience.


                                To learn more, see our tips on writing great answers.




                                draft saved


                                draft discarded














                                StackExchange.ready(
                                function () {
                                StackExchange.openid.initPostLogin('.new-post-login', 'https%3a%2f%2fbioinformatics.stackexchange.com%2fquestions%2f5616%2fimporting-gff-file-with-biopython%23new-answer', 'question_page');
                                }
                                );

                                Post as a guest















                                Required, but never shown





















































                                Required, but never shown














                                Required, but never shown












                                Required, but never shown







                                Required, but never shown

































                                Required, but never shown














                                Required, but never shown












                                Required, but never shown







                                Required, but never shown







                                Popular posts from this blog

                                "Incorrect syntax near the keyword 'ON'. (on update cascade, on delete cascade,)

                                Alcedinidae

                                Origin of the phrase “under your belt”?