How to convert a Map file to BED using perl?

Question

[lexauex]

Hello.

I am new to bioinformatics and this is an elective class. My lab project is to convert MAP to BED. I am using text wrangler to edit the script and I have a MAC.

This is what I have so far:

#!./perl
use strict;
use warnings;
my $input1 = shift @ARGV;
my @output = $input1;
print "$input1= $output\n";

Thank you!

[GenoMax]

You are going to need to do a bit more effort on your own than that to get help with your code. Thank you for clarifying that this is an assignment/project.

[lexauex]

If I knew more, trust me I would have more. Like I stated before, I am new to all of this.

Thank you for taking the time to respond.

Answer 1

[Petr Ponomarenko]

Could you please show example input and example of desired output? plink can convert between map/ped and bed/bim/fam if this is what you are looking for with recode option. Is this what you are looking for to reimplement in your project?

[lexauex]

Here is the Input:

1   rs2905037-G-A   0   775426
1   rs6701114-C-T   0   1022037
2   SNP1-G-T    0   2
10  rs7918734-C-A   0   192533
10  rs1476129-A-C   0   265520
10  rs1476130-T-A   0   274675
10  rs17221239-C-G  0   285113

Output:

chr1    775425  775426  rs2905037-G-A   20
chr1    1022036 1022037 rs6701114-C-T   20
chr2    1   2   SNP1-G-T    20
chr10   192532  192533  rs7918734-C-A   20
chr10   265519  265520  rs1476129-A-C   20
chr10   274674  274675  rs1476130-T-A   20
chr10   285112  285113  rs17221239-C-G  20
chrX    816303  816304  rs17537524-C-A  20
chrX    2335502 2335503 rs17461767-G-A  20
chrY    47  48  SNP2-T-C    20
23  rs17537524-C-A  0   816304
23  rs17461767-G-A  0   2335503
24  SNP2-T-C    0   48

I am currently using text wrangler trying to create a script. Our professor told us to convert the MAP to BED, which I know that I need to use INPUT/OUTPUT codes. I had a shift in place and my professor said that is correct. Do I need to grep any information out? I just really need a kick start. I understand this stuff when given an instructed assignment, but this is free range so no too much information was provided.

Thank you for your advice!

[Petr Ponomarenko]

Thank you, genomax2, for reformatics the lexauex's reply.

This part:

23  rs17537524-C-A  0   816304
23  rs17461767-G-A  0   2335503
24  SNP2-T-C    0   48

does not look like example of proper desired output. Assuming these 3 lines are just a mistake you can use this awk one-liner to the output from input:

awk '{print "chr"$1, $4-1, $4, $2, "20"}' input > output

also I do not understand what "20" means in your output in the fifth column. Please clarify especialy if it does not have to be equal to 20 always for your inputs.

[GenoMax]

It is possible that something may have been lost when @lexauex copy/pasted the sample in. @lexauex: You can edit the post above to change. I agree with @Petr that the last part seems to have some error in it. Assuming this part is correct

chr1    775425  775426  rs2905037-G-A   20
chr1    1022036 1022037 rs6701114-C-T   20
chr2    1   2   SNP1-G-T    20
chr10   192532  192533  rs7918734-C-A   20
chr10   265519  265520  rs1476129-A-C   20
chr10   274674  274675  rs1476130-T-A   20
chr10   285112  285113  rs17221239-C-G  20
chrX    816303  816304  rs17537524-C-A  20
chrX    2335502 2335503 rs17461767-G-A  20
chrY    47  48  SNP2-T-C    20

@Petr's solution will do what you want. It provides a ready to use solution that does not use Perl.

If you are required to do this exercise using perl then see if this pesudocode helps.

• Open the data file, grab the name before .map using split.
• Read the file in line by line. chomp to remove return.
• Split the line in constituent records (on tab or what ever separates the fields)
• Print the reformatted record out (join plus combination of fields from last step) to filename.ped
• Close files

[lexauex]

The output was created by my professor. When I ran the file in the terminal it said there was an error as well. I brought this issue to him and he ensures that there is no mistake. Can I ask why do you believe the end part is an error? I am familiar with split. This has helped me greatly.

Thank you!

[GenoMax]

I feel that the prefix chr is missing from those rows and plus they do not seem to follow the convention of other rows where

chrN start stop rsID-N-N 20 seems to be general format.