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Full Discussion: Parsing the test file
Top Forums Shell Programming and Scripting Parsing the test file Post 302901351 by BCW_123 on Tuesday 13th of May 2014 12:56:49 PM
Old 05-13-2014
Parsing the test file
Hello,

I want to retrieve the rows with uniq count(column 4) for every *ref gene(column 7) on the basis of strand(column8 ) and tss(column 5).
If a ref gene has same number of count and it is on negative strand then keep the row with its highest tss and likewise*
If a ref gene has same number of count and it is on positive strand then keep the row with its lowest tss

I am working on the dat of format:
Code:
CHR	TSS-25bp	TSS+25bp	count 	tss	Ensemble transcript	refgene	strand
chr15	79554474	79554524	2	79554499	ENSMUST00000089311	Sun2	-
chr15	79554475	79554525	2	79554500	ENSMUST00000100439	Sun2	-
chr15	79554477	79554527	2	79554502	ENSMUST00000046259	Sun2	-
chr15	79569054	79569104	1	79569079	ENSMUST00000159660	Sun2	-
chr15	79570243	79570293	4	79570268	ENSMUST00000160355	Sun2	-
chr17	44914075	44914125	2	44914100	ENSMUST00000050630	Supt3h	+
chr17	44914248	44914298	3	44914273	ENSMUST00000130623	Supt3h	+
chr17	44914319	44914369	3	44914344	ENSMUST00000127798	Supt3h	+
chr11	87551028	87551078	2	87551053	ENSMUST00000152700	Supt4h1	+
chr11	87551029	87551079	2	87551054	ENSMUST00000141169	Supt4h1	+
chr7	29099891	29099941	2	29099916	ENSMUST00000003527	Supt5h	-
chr11	78020504	78020554	3	78020529	ENSMUST00000108314	Supt6h	-



I would expect this in the output:
Code:
CHR	TSS-25bp	TSS+25bp	count 	tss	Ensemble transcript	refgene	strand
chr15	79554477	79554527	2	79554502	ENSMUST00000046259	Sun2	-
chr15	79569054	79569104	1	79569079	ENSMUST00000159660	Sun2	-
chr15	79570243	79570293	4	79570268	ENSMUST00000160355	Sun2	-
chr17	44914075	44914125	2	44914100	ENSMUST00000050630	Supt3h	+
chr17	44914248	44914298	3	44914273	ENSMUST00000130623	Supt3h	+
chr11	87551028	87551078	2	87551053	ENSMUST00000152700	Supt4h1	+
chr7	29099891	29099941	2	29099916	ENSMUST00000003527	Supt5h	-
chr11	78020504	78020554	3	78020529	ENSMUST00000108314	Supt6h	-


So far I have this ,
Code:


Code:



#!/bin/bash

example=Workbook4.txt
for gene in `cut -f7 example | uniq`
** do
** sign=`grep $gene example | cut -f8 | uniq`
** for count in `grep $gene example | cut -f4 | sort | uniq`
** do
* * * if [ "$sign" == "-" ]
* * * then
* * * grep $gene example | grep $count example | sort -k5 | head -1 ----
* * * else
* * * grep $gene example | grep $count example | sort -k5 | tail -1 ----
** done
** break
done

]

I am not sure about the one in bold. It would be nice if you can help me solving this.*

Thanks for your time
Kirthi

Moderator's Comments:
Mod Comment Please use code tags next time for your code and data. Thanks
Last edited by BCW_123; 05-13-2014 at 02:16 PM.. Reason: code tags
 

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