I am trying to take a list of text files (which have the extension .annotation but are still text files) and merge them together into one file. I also want to create a new column with the original file name so I can later sort the table by file name.
I have a list of files that look like this -
> read.table("Sample2-1_nucleotideRate.annotation")
V1 V2 V3 V4 V5 V6 V7 V8 V9 V10
1 pJW316-17_beforeNGS non-coding 29 29 G A 0.9657791941 NA NA <NA>
2 pJW316-17_beforeNGS non-coding 54 299 A G 0.0064375000 NA NA <NA>
3 pJW316-17_beforeNGS non-coding 64 349 T C 0.0111019737 NA NA <NA>
4 pJW316-17_beforeNGS nsps 85 644 A G 0.0044375000 9 3 synonymous>K
I would like a new file to look like this -
> read.csv("all_data.csv", header = T)
X samplename X.region feature position coverage reference alternate alt_frequency CDS_position AA_position AA_change
1 1 Sample2-1 pJW316-17_beforeNGS non-coding 29 29 G A 0.965779194 NA NA <NA>
2 2 Sample2-1 pJW316-17_beforeNGS non-coding 54 299 A G 0.006437500 NA NA <NA>
3 3 Sample2-1 pJW316-17_beforeNGS non-coding 64 349 T C 0.011101974 NA NA <NA>
4 4 Sample2-1 pJW316-17_beforeNGS nsps 85 644 A G 0.004437500 9 3 synonymous>K
5 5 Sample2-1 pJW316-17_beforeNGS nsps 96 808 A G 0.003437500 20 7 D
