Question: GenPept(.gp) file to (.csv) excel file conversion
gravatar for easyshortcatchy
3.0 years ago by
easyshortcatchy0 wrote:

I am trying to convert a GenPept(.gp) file of blast results into a csv file to view in excel. I am thinking I may be able to do It with a text editor but I was wondering if there is an easier less human error prone way. Just as a side note, yes I know BLAST exports a csv file of the hit table but what I want is a neat table of each of the hits with their name, order, ID and sequence, the BLAST csv only gives the ID in a very combined and confusing manner with all the BLAST search statistics.

Any other advice to self teaching yourself bioinformatics is welcome.

software error • 1.2k views
ADD COMMENTlink written 3.0 years ago by easyshortcatchy0

Hmm. GenPept format should be for protein sequence. How did you manage to get blast results in that format?

ADD REPLYlink written 3.0 years ago by genomax76k

I did blastp and I selected all results clicked GenPept it took me to the search page and I selected send to then file then GenPept. The main reason I want the GenPept is because I will need the associated pubmed articles for later on, but right now I just want to turn several of the Important sub parts into a table so I will end up with a table listing the sequence, its accesion number, its description, what species and what order of mammal. Like I said I plan to attempt to do this by text editing to make it a csv but it being a large file I am worried the terms I use will be to general and end up parsing things incorrectly.

ADD REPLYlink written 3.0 years ago by easyshortcatchy0

Ah so you downloaded the blast results in GenPept sequence format. SeqIO from BioPython should be able to parse these files.

ADD REPLYlink written 3.0 years ago by genomax76k

I don't have a lot of experience with python but I have some decent experience with R, hopefully I will be able to figure it out, thanks for the help from what I can tell it looks like the function will do what I need I just have to figure out how to write to files in python.

ADD REPLYlink written 3.0 years ago by easyshortcatchy0

If you are an R fan then perhaps this will work.

ADD REPLYlink written 3.0 years ago by genomax76k
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