Question

software or R package to change protein *.msf file to any readable file

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4.0 years ago

yueli7 ▴ 250

Hello

I have some protein *.msf file. I can not open it.

Which software or R package that can change this kind of *.msf to any readable file?

Thanks in advance for great help!

Best,

Yue

software error • 1.7k views

ADD COMMENT • link updated 10 months ago by realpopeofchillitown • 0 • written 4.0 years ago by yueli7 ▴ 250

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How was this file generated? What does the command file <filename>.msf return? Have you tried head, more and less on the file?

Also, how is the software error tag relevant here?

ADD REPLY • link 4.0 years ago by Ram 44k

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Hello RamRS,

Thank you so much for your great help!

I think it is a SQLite database.

Thank you again!

Best,

Yue

-p0xxx:~$ file OstromR_Set7_Enriched.msf 
OstromR_Set7_Enriched.msf: SQLite 3.x database, last written using SQLite version 3007011

ADD REPLY • link 4.0 years ago by yueli7 ▴ 250

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If this is related to your prior question then you need to show output of things @RamRS has asked: change *.msf file into excel file

ADD REPLY • link 4.0 years ago by GenoMax 147k

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From this, it is apparent that the msf file is a database that can be opened in SQLite. OP should be looking for R packages that can read in SQLite DBs, such as RSQLite: https://db.rstudio.com/databases/sqlite/

ADD REPLY • link 4.0 years ago by Ram 44k

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Hello RamRS,

Thank you so much for your great help!

Best,
Yue

ADD REPLY • link updated 10 months ago by Ram 44k • written 4.0 years ago by yueli7 ▴ 250

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Hi @yueli7,

Did you happen to figure out the database schema for these msf files to be used via sqllite?

I'm trying to look at the tables but there are way too many times to manually figure out the schema.

Any pointers are highly appreciated.

Thanks!

ADD REPLY • link 10 months ago by realpopeofchillitown • 0

score 0 · Answer 1 · 2020-11-25

If you are talking about sequence alignments in MSF format (sometimes called GCG format), those are plain text files that could be viewed in any text editor. There are many ways to convert them: