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Re: Find duplicate based on specific fields while allowing 2 mismatch

by shadowsong (Monk)
on Aug 28, 2017 at 11:05 UTC ( #1198147=note: print w/replies, xml ) Need Help??


in reply to Find duplicate based on specific fields while allowing 2 mismatch

Hi amitgsir

Not wanting to assume what your criteria is for UMIs that comprise a cluster; could you expand on what you mean by:

2. Column 3 must also be similar, i.e. in each cluster lines with similar UMI allowing 2 mismatch will be clustered together

We need a bit more to go on:

  1. What do the [up to 3] UMIs need to have in common to be considered similar?
  2. Why is TCACGGTG in the first cluster instead of TCAAAATG?

If it's all the same and it doesn't matter what the UMIs are as long as you have them in sets of 3s; you could try this:

#!perl -slw use strict; my ($chromosomes,$DELIMITER) = (undef,'CLUSTER'); while ( <DATA> ) { s/\R//g; # remove line breaks; my $record = [split /\s+/]; push @{$chromosomes->{$record->[0]}->{$record->[2]}},[$record->[1] +,$record->[3]]; } foreach my $chrM (sort keys %{$chromosomes}) { my $cnt = 0; # used to print delimiter foreach my $UMI (sort {$a cmp $b} keys %{$chromosomes->{$chrM}}) { print $DELIMITER unless $cnt++ % 3; print "$chrM\t$_->[0]\t$UMI\t$_->[1]" foreach (sort {$a->[0] <=> $b->[0] or $a->[1] <=> $b->[1]} @{$chromosomes->{$chrM}->{$UMI +}}); } } __DATA__ chrM:307 0 AGCGGGGA 129 chrM:307 0 AGCGGGGA 130 chrM:307 0 AGCGGGGA 129 chrM:308 0 AGCGGGGA 129 chrM:308 0 AGCGGGGA 130 chrM:308 0 AGCGGGGA 129 chrM:309 0 AGCGGGGA 129 chrM:309 0 AGCGGGGA 130 chrM:309 0 AGCGGGGA 129 chrM:307 0 TCAAAATG 130 chrM:308 0 TCAAAATG 130 chrM:309 0 TCAAAATG 130 chrM:307 0 TCACGGTG 130 chrM:308 0 TCACGGTG 130 chrM:309 0 TCACGGTG 130 chrM:307 0 TCAGCCTG 129 chrM:308 0 TCAGCCTG 129 chrM:309 0 TCAGCCTG 129 chrM:307 0 TCAGGGAG 130 chrM:308 0 TCAGGGAG 130 chrM:309 0 TCAGGGAG 130 chrM:307 1 TCAGGGTG 106 chrM:307 2 TCAGGGTG 130 chrM:307 2 TCAGGGTG 129 chrM:308 1 TCAGGGTG 106 chrM:308 2 TCAGGGTG 130 chrM:308 2 TCAGGGTG 129 chrM:309 1 TCAGGGTG 106 chrM:309 2 TCAGGGTG 130 chrM:309 2 TCAGGGTG 129

Output

C:\code\perlmonks>perl pm_1198131.pl CLUSTER chrM:307 0 AGCGGGGA 129 chrM:307 0 AGCGGGGA 129 chrM:307 0 AGCGGGGA 130 chrM:307 0 TCAAAATG 130 chrM:307 0 TCACGGTG 130 CLUSTER chrM:307 0 TCAGCCTG 129 chrM:307 0 TCAGGGAG 130 chrM:307 1 TCAGGGTG 106 chrM:307 2 TCAGGGTG 129 chrM:307 2 TCAGGGTG 130 CLUSTER chrM:308 0 AGCGGGGA 129 chrM:308 0 AGCGGGGA 129 chrM:308 0 AGCGGGGA 130 chrM:308 0 TCAAAATG 130 chrM:308 0 TCACGGTG 130 CLUSTER chrM:308 0 TCAGCCTG 129 chrM:308 0 TCAGGGAG 130 chrM:308 1 TCAGGGTG 106 chrM:308 2 TCAGGGTG 129 chrM:308 2 TCAGGGTG 130 CLUSTER chrM:309 0 AGCGGGGA 129 chrM:309 0 AGCGGGGA 129 chrM:309 0 AGCGGGGA 130 chrM:309 0 TCAAAATG 130 chrM:309 0 TCACGGTG 130 CLUSTER chrM:309 0 TCAGCCTG 129 chrM:309 0 TCAGGGAG 130 chrM:309 1 TCAGGGTG 106 chrM:309 2 TCAGGGTG 129 chrM:309 2 TCAGGGTG 130

Cheers
Shadowsong

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