Collapsing and counting by key column in a sorted file Post: 302536924

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Top Forums Shell Programming and Scripting Collapsing and counting by key column in a sorted file Post 302536924 by ramouz87 on Wednesday 6th of July 2011 01:38:51 PM

07-06-2011

Registered User

Collapsing and counting by key column in a sorted file

Hi
I have a tab separated file with reads mappings of more than 2 million reads> the file is sorted by ID and looks like the following:

SeqID	Seq	FreqSeq	PosSeq
HWI-EA332_0036:5:100:10131:16361#ATGC/1	GACTTGAGGTCTCCCCCGCA	1	TZRTMR_40497:317:+
HWI-EA332_0036:5:100:10131:16361#ATGC/1	GACTTGAGGTCTCCCCCGCA	1	YSXAZZ_40497:317:+
HWI-EA332_0036:5:100:10131:16361#ATGC/1	GACTTGAGGTCTCCCCCGCA	1	AZZOL148119:523:+
HWI-EA332_0036:5:100:10131:16361#ATGC/1	GACTTGAGGTCTCCCCCGCA	1	VCXT148119:523:+
HWI-EA332_0036:5:100:10554:9799#ATGC/1	GACTCCTAAATTAACAACAA	1	YSXAZZ_35135:573:+
HWI-EA332_0036:5:100:10554:9799#ATGC/1	GACTCCTAAATTAACAACAA	1	TZRTMR_35135:573:+
HWI-EA332_0036:5:100:10791:13901#ATGC/1	GACTAGTGAGTGACCCGCTC	1	TZRTMR_7034:497:+
HWI-EA332_0036:5:100:10791:13901#ATGC/1	GACTAGTGAGTGACCCGCTC	1	YSXAZZ_7034:497:+
HWI-EA332_0036:5:100:11825:11517#ATGC/1	GACTAATATAAATAAGTCTC	1	YSXAZZ_3676:148:+
HWI-EA332_0036:5:100:11825:11517#ATGC/1	GACTAATATAAATAAGTCTC	1	TZRTMR_3676:148:+
HWI-EA332_0036:5:100:11825:11517#ATGC/1	GACTAATATAAATAAGTCTC	1	TZRTMR_2085:139:+
HWI-EA332_0036:5:100:11825:11517#ATGC/1	GACTAATATAAATAAGTCTC	1	YSXAZZ_2085:139:+
HWI-EA332_0036:5:100:13509:3643#ATGC/1	GACTACCCGCCAAACCCCAG	2	YTTSTZ_566255:526:-
HWI-EA332_0036:5:100:13509:3643#ATGC/1	GACTACCCGCCAAACCCCAG	2	YYTWQ_566255:526:-
HWI-EA332_0036:5:100:13837:1118#ATGC/1	GACTCCCGCATCCCGCAAAC	1	PZXVXZ_21909:999:+
HWI-EA332_0036:5:100:13837:1118#ATGC/1	GACTCCCGCATCCCGCAAAC	1	TZRTMR_21909:999:+

And I would like to collapse the columns [3,4] having the same ID to get a table like this :

SeqID	Seq	FreqSeq	PosSeq	N_UpT
HWI-EA332_0036:5:100:10131:16361#ATGC/1	GACTTGAGGTCTCCCCCGCA	1,1,1,1	TZRTMR_40497:317:+,YSXAZZ_40497:317:+,AZZOL148119:523:+,VCXT148119:523:+	4
HWI-EA332_0036:5:100:10554:9799#ATGC/1	GACTCCTAAATTAACAACAA	1,1	YSXAZZ_35135:573:+,TZRTMR_35135:573:+	2
HWI-EA332_0036:5:100:10791:13901#ATGC/1	GACTAGTGAGTGACCCGCTC	1,1	TZRTMR_7034:497:+,YSXAZZ_7034:497:+	2
HWI-EA332_0036:5:100:11825:11517#ATGC/1	GACTAATATAAATAAGTCTC	1,1,1,1	YSXAZZ_3676:148:+,TZRTMR_3676:148:+,TZRTMR_2085:139:+,YSXAZZ_2085:139:+	4
HWI-EA332_0036:5:100:13509:3643#ATGC/1	GACTACCCGCCAAACCCCAG	2,2	YTTSTZ_566255:526:-,YYTWQ_566255:526:-	2
HWI-EA332_0036:5:100:13837:1118#ATGC/1	GACTCCCGCATCCCGCAAAC	1,1	PZXVXZ_21909:999:+,TZRTMR_21909:999:+	2

The column 2 is unique as well and the N_UpT is the count of number of lines matched by the id.

Any help idea about the best way of doing this (in AWK ? Perl ?) would be much appreciated.
Thanks in advance for the help and suggestions.
Best,
Ramzi

ramouz87

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