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Top Forums Shell Programming and Scripting Convert rows to columns based on condition Post 302843972 by Jotne on Friday 16th of August 2013 01:39:50 AM
Old 08-16-2013
Try this
Code:
awk '
	/^GN/ {split($0,a,"[=;]");printf "\n%s|",a[2]}
	/^RC/ {split($0,a,"=");printf a[2];f=1}
	/^CC/ {if (f) {printf "|"};sub(/-!- FUNCTION:/,x);split($0,a,"  +");printf "%s ",a[2];f=0}
END {print ""}' uniprot_human_prts_with_tissue_fn

Every field is now separated by |, in TISSUE its separated by ;
What should we do with the Synonyms field? Print it, where?

3 first line:
Code:
YWHAB|Keratinocyte;Thymus;Skin;Colon carcinoma;Platelet;Melanoma;Leukemic T-cell;|Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner. Negative regulator of osteogenesis. Blocks the nuclear translocation of the phosphorylated form (by AKT1) of SRPK2 and antagonizes its stimulatory effect on cyclin D1 expression resulting in blockage of neuronal apoptosis elicited by SRPK2.
YWHAE|Liver;Brain;Heart;Caudate nucleus, Heart, and Subthalamic nucleus;Placenta;Platelet;B-cell lymphoma;Histiocytic lymphoma;Brain, and Cajal-Retzius cell;Melanoma;Liver;Cervix carcinoma;|Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner.
YWHAH|Brain;Brain;Lymph;Keratinocyte;Platelet;Platelet;Leukemic T-cell;|Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner. Negatively regulates the kinase activity of PDPK1.


EDIT: Here synonyms are printed behind original like: YWHAH-YWHA1
Code:
awk '
	/^GN/ {split($0,a,"[=;]");p=(a[4])?a[2]"-"a[4]:a[2];printf "\n%s|",p}
	/^RC/ {split($0,a,"=");printf a[2];f=1}
	/^CC/ {if (f) {printf "|"};sub(/-!- FUNCTION:/,x);split($0,a,"  +");printf "%s ",a[2];f=0}
END {print ""}' uniprot_human_prts_with_tissue_fn

Code:
YWHAB|Keratinocyte;Thymus;Skin;Colon carcinoma;Platelet;Melanoma;Leukemic T-cell;|Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner. Negative regulator of osteogenesis. Blocks the nuclear translocation of the phosphorylated form (by AKT1) of SRPK2 and antagonizes its stimulatory effect on cyclin D1 expression resulting in blockage of neuronal apoptosis elicited by SRPK2.
YWHAE|Liver;Brain;Heart;Caudate nucleus, Heart, and Subthalamic nucleus;Placenta;Platelet;B-cell lymphoma;Histiocytic lymphoma;Brain, and Cajal-Retzius cell;Melanoma;Liver;Cervix carcinoma;|Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner.
YWHAH-YWHA1|Brain;Brain;Lymph;Keratinocyte;Platelet;Platelet;Leukemic T-cell;|Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner. Negatively regulates the kinase activity of PDPK1.


Last edited by Jotne; 08-16-2013 at 02:48 AM..
This User Gave Thanks to Jotne For This Post:
 

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