SOAPsnp sort script

[jgibbons1]

Hi all,
For anyone familiar with the SOAP package...
SOAPsnp takes the SOAPaligner output as its input. The only issue here is that the SOAPaligner output has to be slightly modified. The output has to be sorted first by chromosome name (alphabetically) then by chromosome coordinate (numerically). The output contains 13 tab delimited columns. Chromosome name is the 8th column and coordinate is the 9th.

My perl skills are still infantile and I'm having a tough time formatting my data.
Does anyone have a script they wouldn't mind sharing or a solution to this?

Here is an example line of the output:
SRR003674.68 GATTAAATAAATATATAGATACCTTTTCCTACTTAT ,)4E8)*;/,.914+-+,&+&)+(+$%($"($#$&# 1 a 36 + Scer_gi|93117368|ref|NC_001136.8| 1272821 2 T->31C-28 T->28C-28 36M 28T2T4
SRR003674.113 GATATGCTTGAGGATGAACGAGAAGCTAATATAGTC '%&%%%"&$&#)*)(++(+-0+1+'++(104-2-)0 1 a 36 - Scer_gi|93117368|ref|NC_001136.8| 1277159 2 G->6C-30 A->7T-26 36M 6GA28


Thanks in advance...

[jgibbons1]

this has been working in a unix environment

sort -k [column number] [filename] > outfile

[jgibbons1]

In case anyone is interested...here's a way using unix commands

(1) From your SOAPaligner output, make a new file for each chromosome using GREP

grep -w "chr_1" OUTPUT.soap > chr1_OUTPUT.soap
grep -w "chr_2" OUTPUT.soap > chr2_OUTPUT.soap
grep -w "chr_3" OUTPUT.soap > chr3_OUTPUT.soap
etc...

(2) For each individual chromosome file sort by the chromosomal coordinate (which in this case is the 9th column) using the SORT command

sort -k 9 -n chr1_OUTPUT.soap > chr1_OUTPUT_sorted.soap
sort -k 9 -n chr2_OUTPUT.soap > chr2_OUTPUT_sorted.soap
sort -k 9 -n chr3_OUTPUT.soap > chr3_OUTPUT_sorted.soap
etc...

(3) Concatenate the outputs into a single file
cat chr1_OUTPUT_sorted.soap > OUTPUT_sorted.soap
cat chr2_OUTPUT_sorted.soap >> OUTPUT_sorted.soap
cat chr3_OUTPUT_sorted.soap >> OUTPUT_sorted.soap

OUTPUT_sorted.soap can now be used as the input file in SOAPsnp

Functional but not that elegant...

[kmcarr]

You can do this with a single unix sort command.

sort -k8,8 -k9,9n OUTPUT.soap > OUTPUT_sorted.soap

[jgibbons1]

Thanks!

When priority sorting there seems to be a memory issue. Breaking the output into individual chromosomes seemed ease that.