mbk0asis · January 5, 2017 10:19
diff --git a/extracting COSMIC cDNA mutation data b/extracting COSMIC cDNA mutation data
 grep -Po 'c..*' COSMIC_TP53_MUT | sed 's/;/\t/g' | cut -f 1,3 | sed 's/CNT=//g'| grep -Po 'c.\d*(\_?\-?\+?)\d*' > position

 grep -Po 'c..*' COSMIC_TP53_MUT | sed 's/;/\t/g' | cut -f 1,3 | sed 's/CNT=//g'| grep -Po '[a-zA-Z]*\>?[a-zA-Z]*\t' > sequence

 grep -Po 'c..*' COSMIC_TP53_MUT | sed 's/;/\t/g' | cut -f 3 | sed 's/CNT=//g' > count

 paste position sequence count | sed 's/c.//g' > COSMIC_TP53_MUT_all
	grep -Po 'c..' COSMIC_TP53_MUT \| sed 's/;/\t/g' \| cut -f 1,3 \| sed 's/CNT=//g'\| grep -Po 'c.\d(\_?\-?\+?)\d*' > position

	grep -Po 'c..' COSMIC_TP53_MUT \| sed 's/;/\t/g' \| cut -f 1,3 \| sed 's/CNT=//g'\| grep -Po '[a-zA-Z]\>?[a-zA-Z]*\t' > sequence

	grep -Po 'c..*' COSMIC_TP53_MUT \| sed 's/;/\t/g' \| cut -f 3 \| sed 's/CNT=//g' > count

	paste position sequence count \| sed 's/c.//g' > COSMIC_TP53_MUT_all