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In f1 below I am trying to split $1 based on each line and create a bed file. If the line is a snp then the : is spilt and the text is $1 the last digit is $2 -1 and $3 and the letter to the left of the > is $4 and the letter to the right is $5. (lines 1 and 2)

If the line has dup then the : is spilt and the text is $1 the last digit is $2 and $3 and the $4 is - and the letter to the right is $5. (line 4)

If the line has del with nothing else then the : is spilt and the text is $1 the last digit is $2 and $3 and the letter to the left of the > is $4 and $5 is -. (line 5)

I am not sure how to format for line 3 (the complex indel)... maybe split $1 on the : and the text is $1 the last digit is $2 and $3 and the letters to the left of the > is $4 and the letters to the right is $5. Thank you :)

f1

chr7:140453145A>T
chr7:140453136A>T 
chr7:140453135_140453136delCAinsTT
chr20:31022287dupA
chr19:13054614delG

desired

chr7 140453144 140453145 A T 
chr7 140453135 140453136 A T 
chr7 140453135 140453136 TT CA
chr20 31022287 31022287 - A
chr19 13054614 13054614 G -

awk

awk 'BEGINOFS="t" sub(/[^0-9]+$/, "", $1)' f1

awk 'BEGIN FS = "[ -]"; OFS="t" NF==3 print $1, $2 - 1, $2, $3 NF==4 print $1, $2, $3, $4 ' f1

The following Python script seems to do the job.

#!/usr/bin/env python3

from __future__ import print_function
import re
import sys

for line in sys.stdin:
 if '_' in line:
 match = re.search(r'(S+):(d+)_(d+)del([ACGT]+)ins([ACGT]+)', line)
 print(match.group(1), match.group(2), match.group(3), match.group(5), match.group(4), sep='t')
 elif 'dup' in line or 'del' in line:
 match = re.search(r'(S+):(d+)(del|dup)([ACGT]+)', line)
 if match.group(3) == 'del':
 print(match.group(1), match.group(2), match.group(2), match.group(4), '-', sep='t')
 else:
 print(match.group(1), match.group(2), match.group(2), '-', match.group(4), sep='t')
 else:
 match = re.search(r'(S+):(d+)([ACGT]+)>([ACGT]+)', line)
 coord = int(match.group(2))
 print(match.group(1), coord - 1, coord, match.group(3), match.group(4), sep='t')

Invoked like so on the command line.

[standage@lappy ~] $ ./transform < f1
chr7 140453144 140453145 A T
chr7 140453135 140453136 A T
chr7 140453135 140453136 TT CA
chr20 31022287 31022287 - A
chr19 13054614 13054614 G -

The Python script in my first response is heavy on regex matching, which is pretty clunky in Python. I like Python much better than Perl overall, but a throwaway script like this will be clearer and more concise in Perl.

#!/usr/bin/env perl
use strict;

while(<STDIN>) dup)([ACGT]+)/) 
 if ($3 eq "del") 
 print("$1t$2t$2t$4t-n");
 
 else 
 print("$1t$2t$2t-t$4n");
 
 
 elsif (m/(S+):(d+)([ACGT]+)>([ACGT]+)/) 
 my $coord2 = $2;
 my $coord1 = $2 - 1;
 print("$1t$coord1t$coord2t$3t$4n")
 

It's been several years since I wrote Perl on a regular basis, so there are probably ways to make the script even more clear and concise. (Although I have a love/hate relationship with the default/hidden variables, which can make a script more concise but also harder for a newcomer to understand.)

Invoked like so on the command line.

[standage@lappy ~] $ ./transform < f1
chr7 140453144 140453145 A T
chr7 140453135 140453136 A T
chr7 140453135 140453136 TT CA
chr20 31022287 31022287 - A
chr19 13054614 13054614 G -

Here is an R solution, would probably be slower than the suggested Python solution though:

bed <- readLines("bed.txt")

res <- data.frame()

for(i in bed) 

 temp <- strsplit(i, ":") %>% unlist()

 # case N>N

 if(grepl(">", temp[[2]])) 

 begin <- str_extract(temp[[2]], pattern = "^[:digit:]+") %>% as.integer() - 1
 end <- begin + 1
 ref <- str_extract(temp[[2]], pattern = "[A-Z]")
 alt <- str_extract(temp[[2]], pattern = "[A-Z]$")

 temp_res <- data.frame(temp[[1]], begin, end, ref, alt)
 res <- rbind(res, temp_res)
 

 # case del_ins

 if(grepl("ins", temp[[2]])) 

 begin <- str_extract(temp[[2]], pattern = "^[:digit:]+") %>% as.integer()
 end <- str_extract(temp[[2]], pattern = "_[:digit:]+")
 end <- substring(end, 2, nchar(end)) %>% as.integer()
 ref <- str_extract(temp[[2]], pattern = "[A-Z]+$")
 alt <- str_extract(temp[[2]], pattern = "[A-Z]+")

 temp_res <- data.frame(temp[[1]], begin, end, ref, alt)
 res <- rbind(res, temp_res)
 


 # case dup

 if(grepl("dup", temp[[2]])) 

 begin <- str_extract(temp[[2]], pattern = "^[:digit:]+") %>% as.integer()
 end <- begin
 ref <- "-"
 alt <- str_extract(temp[[2]], pattern = "[A-Z]$")

 temp_res <- data.frame(temp[[1]], begin, end, ref, alt)
 res <- rbind(res, temp_res)
 

 # case del only

 if(grepl("del", temp[[2]]) & !grepl("ins", temp[[2]])) 

 begin <- str_extract(temp[[2]], pattern = "^[:digit:]+") %>% as.integer()
 end <- begin
 ref <- str_extract(temp[[2]], pattern = "[A-Z]$")
 alt <- "-"

 temp_res <- data.frame(temp[[1]], begin, end, ref, alt)
 res <- rbind(res, temp_res)
 



print(res)

 temp..1.. begin end ref alt
1 chr7 140453144 140453145 A T
2 chr7 140453135 140453136 A T
3 chr7 140453135 140453136 TT CA
4 chr20 31022287 31022287 - A
5 chr19 13054614 13054614 G -