how to format a large txt file to bed - awk

Question

I am trying to format CpG methylation calls from R package "methyKit" to simple bed format. Since it is a large file, i can not do it in Excel. I also tried Seqmonk, but it does not allow me to export the data in the format I want. Linux Awk/sed might be a good option, but I am new to them as well. Basically, I need to trim "chr" column, add "stop" column, convert "F" to "+" /"R" to "-", and freqC with 2 decimal places. Can you please help?
From:
chrBase chr base strand coverage freqC freqT
chr1.339 chr1 339 F 7 0.00 100.00
chr1.183 chr1 183 R 4 0.00 100.00
chr1.192 chr1 192 R 6 0.00 100.00
chr1.340 chr1 340 R 5 40.00 60.00
chr1.10007 chr1 10007 F 13 53.85 46.15
chr1.10317 chr1 10317 F 8 0.00 100.00
chr1.10346 chr1 10346 F 9 88.89 11.11
chr1.10349 chr1 10349 F 9 88.89 11.11
To:
chr start stop freqc Coverage strand
1 67678 67679 0 3 -
1 67701 67702 0 3 -
1 67724 67725 0 3 -
1 67746 67747 0 3 -
1 67768 67769 0.333333 3 -
1 159446 159447 0 3 +
1 162652 162653 0 3 +
1 167767 167768 0.666667 3 +
1 167789 167790 0.666667 3 +
1 167797 167798 0 3 +

Answer 1

This should do what you actually want, producing a BED6 file with the methylation percentage in the score column:
$ cat foo.awk
BEGIN{OFS="\t"}
{if(NR>1) {
if($4=="F") {
strand="+"
} else {
strand="-"
}
chromUse=gsub("chr", "", $2);
print chromUse,$3-1,$3,$1,$6,strand,$5
}}
That would then be run with:
awk -f foo.awk input.txt > output.bed
The additional column 7 is the coverage, since genome viewers will only display a single score column:
1 338 339 chr1.339 0.00 + 7
1 182 183 chr1.183 0.00 - 4
1 191 192 chr1.192 0.00 - 6
1 339 340 chr1.340 40.00 - 5
1 10006 10007 chr1.10007 53.85 + 13
1 10316 10317 chr1.10317 0.00 + 8
1 10345 10346 chr1.10346 88.89 + 9
1 10348 10349 chr1.10349 88.89 + 9
You can tweak that further as needed.

Answer 2

It is not entirely clear the exact sequence you want since your "From" data does not correspond to what you show as your "To" results, but if what you are showing is the general format change and in the "From" data, you want to:
discard field 1,
retrieve the "chr" value from the end of field 2,
if the 4th field is "F" make it "+" else if it is "R" make it "-" otherwise leave it unchanged,
use the 3rd field as "start" and 3rd + 1 as "stop" (adjust whether to add or subtract 1 as needed to get the desired "start" and "stop" values),
print 6th field as "freqc",
output 5th field as "Coverage", and finally
output modified 4th field as "strand"
If that is your goal, then with your from data in the file named from, you can do something like the following:
awk '
BEGIN { OFS="\t"; print "chr","start","stop","freqc","Coverage","strand" }
FNR > 1 {
match($2, /[[:digit:]]+$/, arr)
if ($4 == "F")
$4 = "+"
else if ($4 == "R")
$4 = "-"
print arr[0], $3, $3 + 1, $6, $5, $4
}
' from
Explanation, the BEGIN rule is run before awk starts processing records (lines) from the file. Above it simply sets the Output Field Separator to tab and prints the heading.
The condition (pattern) of FNR > 1 on the second rule processes the from file from the 2nd record (line) on (skipping the heading row). FNR is awk's way of saying File Record Number (even though it looks like the N and R are backwards).
match($2, /[[:digit:]]+$/, arr) splits the trailing digits from the second field into the first element of arr (e.g. arr[0]) and not relevant here sets the RSTART and RLENGTH internal variables telling you which character the first digit starts on and how many digits there are.
The if and else if statement does the "F" to "+" and "R" to "-" change. And, finally, the print statement just prints the modified values and unchanged fields in the order specified above.
Example Output
Running the above on your original "From" data will produce:
chr start stop freqc Coverage strand
1 339 340 0.00 7 +
1 183 184 0.00 4 -
1 192 193 0.00 6 -
1 340 341 40.00 5 -
1 10007 10008 53.85 13 +
1 10317 10318 0.00 8 +
1 10346 10347 88.89 9 +
1 10349 10350 88.89 9 +
Let me know if this is close to what you explained in your question, and if not, drop a comment below.
The GNU Awk User's Guide is a great gawk/awk reference.