Re: [Biopython] Biopython Digest, Vol 227, Issue 1
"Riesgo Ferreiro, Pablo" <[email protected]> Mon, 3 Jan 2022 20:36:06 +0000
| Newsgroups | gmane.comp.python.bio.general |
|---|---|
| Message-ID | <[email protected]> |
Dear Ferran, From my experience of querying biomart from python, I found the implementations I used not very intuitive. It seems to me that some details of the biomart REST API (eg: XML) have leaked into the Python API. Maybe having a better Python API around biomart would add some value? Not saying it will be easy... Disclaimer: I am also a newbie in biopython so I would not know how or where this could be integrated. Best wishes, Pablo Riesgo Ferreiro ________________________________ From: Biopython <[email protected]> on behalf of [email protected] <[email protected]> Sent: 03 January 2022 16:06:49 To: [email protected] Subject: Biopython Digest, Vol 227, Issue 1 Send Biopython mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://mailman.open-bio.org/mailman/listinfo/biopython or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of Biopython digest..." Today's Topics: 1. Bioinformatics master's degree final project (Ferran F?bregas) 2. Re: Bioinformatics master's degree final project (T?letch?a St?phane) 3. Re: Bioinformatics master's degree final project (Alexey Morozov) 4. Re: Bioinformatics master's degree final project (Ferran F?bregas) ---------------------------------------------------------------------- Message: 1 Date: Mon, 3 Jan 2022 11:39:40 +0100 From: Ferran F?bregas <[email protected]> To: [email protected] Subject: [Biopython] Bioinformatics master's degree final project Message-ID: <CAAJHJUR_EL=9t1CzAk2UNomR-LjYN_83SmbBcnJ8F-Sbm801jQ@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi! My name is Ferran F?bregas and I'm working on my bioinformatics master?s degree final project. I?m a computer scientist and a Python veteran but a BioPython newbie. I am writing this email because I would like to dedicate the final project of my master's degree in bioinformatics to the development of a library to implement gene annotation, pathway enrichment and access to gene ontologies from Python, similar to how it can be done in R using functions like enrichPathway from ReactomePA or enrichGo from ClusterProfiler. Have any tools been previously developed to do this using BioPython? Are there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or ClusterProfiler? I?m also working on a BioPython GUI based on PySide6. I've seen some old projects related to BioPython GUI development but seem to be discontinued. I would be very happy to use my time to contribute to the bioPython project, and I?m open to any suggestions or ideas. Thanks in advance, Ferran F?bregas -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20220103/a03d1259/attachment-0001.htm> ------------------------------ Message: 2 Date: Mon, 3 Jan 2022 11:49:00 +0100 From: T?letch?a St?phane <[email protected]> To: [email protected] Subject: Re: [Biopython] Bioinformatics master's degree final project Message-ID: <[email protected]> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20220103/2e82ce4c/attachment-0001.htm> ------------------------------ Message: 3 Date: Mon, 3 Jan 2022 19:45:45 +0800 From: Alexey Morozov <[email protected]> To: Ferran F?bregas <[email protected]> Cc: [email protected] Subject: Re: [Biopython] Bioinformatics master's degree final project Message-ID: <CAK=7cMOBFxgJukRDi2fcR2okMABc9DqNN+JCpOOUzZvZS4dhHQ@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Ferran, There is a Python library for GO enrichment called goenrich ( https://github.com/jdrudolph/goenrich). I haven't used it for the last couple of years, but it did its job in 2018 or so (despite lacking some tests available in eg topGO). OTOH, goenrich repo shows that the last commit was in summer 2020, so maybe they've added something. Back when I used it, BioPython integration was basically absent, they just used their own objects for everything. There is also a library called goatools ( https://github.com/tanghaibao/goatools), but I haven't actually used it, so no comments. ??, 3 ???. 2022 ?. ? 18:40, Ferran F?bregas <[email protected]>: > Hi! My name is Ferran F?bregas and I'm working on my bioinformatics > master?s degree final project. I?m a computer scientist and a Python > veteran but a BioPython newbie. > > I am writing this email because I would like to dedicate the final project > of my master's degree in bioinformatics to the development of a library to > implement gene annotation, pathway enrichment and access to gene ontologies > from Python, similar to how it can be done in R using functions like > enrichPathway from ReactomePA or enrichGo from ClusterProfiler. > > Have any tools been previously developed to do this using BioPython? Are > there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or > ClusterProfiler? > > I?m also working on a BioPython GUI based on PySide6. I've seen some old > projects related to BioPython GUI development but seem to be discontinued. > > I would be very happy to use my time to contribute to the bioPython > project, and I?m open to any suggestions or ideas. > > Thanks in advance, > > Ferran F?bregas > _______________________________________________ > Biopython mailing list - [email protected] > https://mailman.open-bio.org/mailman/listinfo/biopython > -- Alexey Morozov, LIN SB RAS, bioinformatics group. Irkutsk, Russia. -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20220103/ab4fda69/attachment-0001.htm> ------------------------------ Message: 4 Date: Mon, 3 Jan 2022 16:06:36 +0100 From: Ferran F?bregas <[email protected]> To: [email protected] Subject: Re: [Biopython] Bioinformatics master's degree final project Message-ID: <CAAJHJUTDdomZWABVB5ZPugC0rO4jm+S7yhC=cw0vUoXZ8a3ovA@mail.gmail.com> Content-Type: text/plain; charset="utf-8" Thanks for your replies, it seems that the community prefers to use different bioinformatics related modules for different functionalities instead of one big, more complex module :) A couple of questions about that: Do you think that it makes sense adding some enrichment functions to biopython? Do you think that it can be useful to create a modular Python GUI that integrates biopython functionalities plus Bioservices / GoEnrich / etc... ? Or maybe it is not useful at all because you can already use some servers like the Galaxy project website (https://galaxyproject.org/)? What do you think about that? Thanks in advance, F On Mon, Jan 3, 2022 at 12:45 PM Alexey Morozov <[email protected]> wrote: > Dear Ferran, > > There is a Python library for GO enrichment called goenrich ( > https://github.com/jdrudolph/goenrich). I haven't used it for the last > couple of years, but it did its job in 2018 or so (despite lacking some > tests available in eg topGO). OTOH, goenrich repo shows that the last > commit was in summer 2020, so maybe they've added something. Back when I > used it, BioPython integration was basically absent, they just used their > own objects for everything. > > There is also a library called goatools ( > https://github.com/tanghaibao/goatools), but I haven't actually used it, > so no comments. > > > ??, 3 ???. 2022 ?. ? 18:40, Ferran F?bregas <[email protected]>: > >> Hi! My name is Ferran F?bregas and I'm working on my bioinformatics >> master?s degree final project. I?m a computer scientist and a Python >> veteran but a BioPython newbie. >> >> I am writing this email because I would like to dedicate the final >> project of my master's degree in bioinformatics to the development of a >> library to implement gene annotation, pathway enrichment and access to gene >> ontologies from Python, similar to how it can be done in R using functions >> like enrichPathway from ReactomePA or enrichGo from ClusterProfiler. >> >> Have any tools been previously developed to do this using BioPython? Are >> there any packages similar to Bioconductor's OrgDb, ReactomePA , GOSeq or >> ClusterProfiler? >> >> I?m also working on a BioPython GUI based on PySide6. I've seen some old >> projects related to BioPython GUI development but seem to be discontinued. >> >> I would be very happy to use my time to contribute to the bioPython >> project, and I?m open to any suggestions or ideas. >> >> Thanks in advance, >> >> Ferran F?bregas >> _______________________________________________ >> Biopython mailing list - [email protected] >> https://mailman.open-bio.org/mailman/listinfo/biopython >> > > > -- > Alexey Morozov, > LIN SB RAS, bioinformatics group. > Irkutsk, Russia. > -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://mailman.open-bio.org/pipermail/biopython/attachments/20220103/b9cbf458/attachment.htm> ------------------------------ Subject: Digest Footer _______________________________________________ Biopython mailing list - [email protected] https://mailman.open-bio.org/mailman/listinfo/biopython ------------------------------ End of Biopython Digest, Vol 227, Issue 1 ***************************************** _______________________________________________ Biopython mailing list - [email protected] https://mailman.open-bio.org/mailman/listinfo/biopython