I'm very early learning to code in R. Is there anyone who can help with a hint on how to do the following task? I don't know how to convert a .faa file into a table, how to select columns, merging tables into one table.
1- Download the following table from the following link https://www.ncbi.nlm.nih.gov/genome/browse/#!/proteins/51/1820449%7CHomo%20sapiens/
2- Select the locus and protein products
3-Download protein sequences in FASTA format (only protein please) https://www.ncbi.nlm.nih.gov/genome/?term=Homo+sapiens
Note: this is a text-like file (80 MB) and you need to convert it into a table, thus you can merge it with the other file.
4- Use these two files to generate a table containing locus, protein products, and protein sequences
Protein products will be shared in both files. You can merge them.
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What have you tried and what is your code so far ?
I have started like that: proteins <-read.csv("https://www.ncbi.nlm.nih.gov/genomes/solr2txt.cgi?q=%5Bdisplay()%5D.from(GenomeProteins).usingschema(%2Fschema%2FGenomeAssemblies).matching(genome_id%3D%3D%5B%2251%22%5D%20and%20genome_assembly_id%3D%3D%5B%221820449%22%5D)&fields=replicon_name%7CName%2Creplicon_accession%7CAccession%2Cstart%7CStart%2Cstop%7CStop%2Cstrand%7CStrand%2Cgene_id%7CGeneID%2Clocus%7CLocus%2Clocus_tag%7CLocus%20tag%2Caccession%7CProtein%20product%2Clength%7CLength%2Cname%7CProtein%20Name&filename=proteins_51_1820449.csv&nolimit=on")
table(proteins$Locus) table(proteins$Protein.product)
Shouldn't this have been covered in class in your course, or where did you get the assignment from?
There is a
mergefunction in R.I have not taken an exact course for this. I just try to develop myself.