I am wanting to use grep/awk/sed to parse a text file containing various gene descriptions.
To download file
wget https://downloads.wormbase.org/releases/current-production-release/species/c_elegans/PRJNA13758/annotation/c_elegans.PRJNA13758.WS283.functional_descriptions.txt.gz
Example text below:
WBGene00000001 aap-1 Y110A7A.10
Concise description: aap-1 encodes the C. elegans ortholog of the phosphoinositide
3-kinase (PI3K) p50/p55 adaptor/regulatory subunit; AAP-1 negatively regulates lifespan
and dauer development, and likely functions as the sole adaptor subunit for the
AGE-1/p110 PI3K catalytic subunit to which it binds in vitro; although AAP-1 potentiates
insulin-like signaling, it is not absolutely required for insulin-like signaling
under most conditions.
Automated description: Enables protein kinase binding activity. Involved in dauer
larval development; determination of adult lifespan; and insulin receptor signaling
pathway. Part of phosphatidylinositol 3-kinase complex. Expressed in intestine and
neurons. Human ortholog(s) of this gene implicated in several diseases, including
Alzheimer's disease; SHORT syndrome; carcinoma (multiple); and immunodeficiency
36. Is an ortholog of human PIK3R3 (phosphoinositide-3-kinase regulatory subunit
3).
Gene class description: phosphoinositide kinase AdAPter subunit
=
WBGene00000002 aat-1 F27C8.1
Concise description: aat-1 encodes an amino acid transporter catalytic subunit;
when co-expressed in Xenopus oocytes with the ATG-2 glycoprotein subunit, AAT-1
is able to facilitate amino acid uptake and exchange, showing a relatively high
affinity for small and some large neutral amino acids; in addition, AAT-1 is able
to covalently associate with ATG-2 or ATG-1 to form heterodimers in the Xenopus
expression system; when co-expressed with ATG-2, AAT-1 localizes to the cell surface
of oocytes, but when expressed alone or with ATG-1, AAT-1 localizes intracellularly.
Automated description: Contributes to L-amino acid transmembrane transporter activity.
Involved in amino acid transmembrane transport. Located in plasma membrane. Part
of amino acid transport complex. Expressed in egg-laying apparatus; head motor neurons;
and tail. Human ortholog(s) of this gene implicated in cystinuria and lysinuric
protein intolerance. Is an ortholog of human SLC7A8 (solute carrier family 7 member
8).
Gene class description: Amino Acid Transporter
=
WBGene00000003 aat-2 F07C3.7
Concise description: aat-2 encodes a predicted amino acid transporter catalytic
subunit; when co-expressed in Xenopus oocytes with a glycoprotein subunit, however,
AAT-2 is not able to induce amino acid uptake.
Automated description: Predicted to enable L-amino acid transmembrane transporter
activity. Predicted to be involved in L-alpha-amino acid transmembrane transport
and L-amino acid transport. Predicted to be located in membrane. Predicted to be
integral component of membrane. Human ortholog(s) of this gene implicated in cystinuria.
Is an ortholog of human SLC7A8 (solute carrier family 7 member 8).
Gene class description: Amino Acid Transporter
This text file contains each gene name (e.g. WBGene00000004 aat-3 F52H2.2a), Concise description:, Automated description:, Gene class description: separated by equal signs "=".
I have been trying to parse this txt file so I figured I start with extracting every column and row (gene) separately. Below is my code
#genes
grep "WBGene" c_elegans.PRJNA13758.WS283.functional_descriptions.txt > WB283_WBgenes.txt
#gene class description:
awk '/Gene class description:/' c_elegans.PRJNA13758.WS283.functional_descriptions.txt > WB283_geneclass.txt
#concise description
awk '
/Concise description:/ { flag=1; pfx="" }
/Automated description/ { flag=0; print "" }
flag { printf "%s%s",pfx,$0; pfx=" " } # assuming appended lines are separated by a single space
' c_elegans.PRJNA13758.WS283.functional_descriptions.txt > WB283_concise.txt
#automated description
awk '
/Automated description:/ { flag=1; pfx="" }
/Gene class description:/ { flag=0; print "" }
flag { printf "%s%s",pfx,$0; pfx=" " } # assuming appended lines are separated by a single space
' c_elegans.PRJNA13758.WS283.functional_descriptions.txt > WB283_automated.txt
MY Problem: is there a way I can combine my code/or new code to better address my problem?
I would like to extract each gene names, Concise description:, Automated description:, and Gene class description: on separate columns and each row representing a gene.
I would like to create a txt file that contains each row as a gene and each column the description choice.
Desired text:
WBGene00000001 aap-1 Y110A7A.10 phosphoinositide kinase AdAPter subunit aap-1 encodes the C. elegans ortholog of the phosphoinositide 3-kinase (PI3K) p50/p55 adaptor/regulatory subunit; AAP-1 negatively regulates lifespan and dauer development, and likely functions as the sole adaptor subunit for the AGE-1/p110 PI3K catalytic subunit to which it binds in vitro; although AAP-1 potentiates insulin-like signaling, it is not absolutely required for insulin-like signaling under most conditions. Enables protein kinase binding activity. Involved in dauer larval development; determination of adult lifespan; and insulin receptor signaling pathway. Part of phosphatidylinositol 3-kinase complex. Expressed in intestine and neurons. Human ortholog(s) of this gene implicated in several diseases, including Alzheimer's disease; SHORT syndrome; carcinoma (multiple); and immunodeficiency 36. Is an ortholog of human PIK3R3 (phosphoinositide-3-kinase regulatory subunit 3).
WBGene00000002 aat-1 F27C8.1 Amino Acid Transporter aat-1 encodes an amino acid transporter catalytic subunit; when co-expressed in Xenopus oocytes with the ATG-2 glycoprotein subunit, AAT-1 is able to facilitate amino acid uptake and exchange, showing a relatively high affinity for small and some large neutral amino acids; in addition, AAT-1 is able to covalently associate with ATG-2 or ATG-1 to form heterodimers in the Xenopus expression system; when co-expressed with ATG-2, AAT-1 localizes to the cell surface of oocytes, but when expressed alone or with ATG-1, AAT-1 localizes intracellularly. Contributes to L-amino acid transmembrane transporter activity. Involved in amino acid transmembrane transport. Located in plasma membrane. Part of amino acid transport complex. Expressed in egg-laying apparatus; head motor neurons; and tail. Human ortholog(s) of this gene implicated in cystinuria and lysinuric protein intolerance. Is an ortholog of human SLC7A8 (solute carrier family 7 member 8).
WBGene00000003 aat-2 F07C3.7 Amino Acid Transporter aat-2 encodes a predicted amino acid transporter catalytic subunit; when co-expressed in Xenopus oocytes with a glycoprotein subunit, however, AAT-2 is not able to induce amino acid uptake. Predicted to enable L-amino acid transmembrane transporter activity. Predicted to be involved in L-alpha-amino acid transmembrane transport and L-amino acid transport. Predicted to be located in membrane. Predicted to be integral component of membrane. Human ortholog(s) of this gene implicated in cystinuria. Is an ortholog of human SLC7A8 (solute carrier family 7 member 8).
CodePudding user response：
Assuming output is tab delimited, one awk idea:
awk '
BEGIN { OFS="\t" }
function print_output() { if (baseID) print baseID,gene_name,trans_name,gene_desc,concise_desc,auto_desc; baseID="" }
$1 ~ /WBGene/ { baseID=$1; gene_name=$2; trans_name=$3 }
/^Gene class description:/ { gene_desc =substr($0, index($0,": ") 2) ; in_block="" }
/^Concise description:/ { concise_desc =substr($0, index($0,": ") 2) ; in_block="concise"; pfx=""; next }
/^Automated description:/ { auto_desc =substr($0, index($0,": ") 2) ; in_block="auto" ; pfx=""; next }
in_block { if (in_block == "concise")
concise_desc = concise_desc pfx $0
else
auto_desc = auto_desc pfx $0
pfx=" "
}
$1 == "=" { print_output() }
END { print_output() }
' input.file
NOTE: yeah, somewhat verbose; can probably be slimmed down a bit but it's the end of my day and I'm out the door ...
For the provided sample this generates:
WBGene00000001 aap-1 Y110A7A.10 phosphoinositide kinase AdAPter subunit aap-1 encodes the C. elegans ortholog of the phosphoinositide 3-kinase (PI3K) p50/p55 adaptor/regulatory subunit; AAP-1 negatively regulates lifespan and dauer development, and likely functions as the sole adaptor subunit for the AGE-1/p110 PI3K catalytic subunit to which it binds in vitro; although AAP-1 potentiates insulin-like signaling, it is not absolutely required for insulin-like signaling under most conditions. Enables protein kinase binding activity. Involved in dauer larval development; determination of adult lifespan; and insulin receptor signaling pathway. Part of phosphatidylinositol 3-kinase complex. Expressed in intestine and neurons. Human ortholog(s) of this gene implicated in several diseases, including Alzheimer's disease; SHORT syndrome; carcinoma (multiple); and immunodeficiency 36. Is an ortholog of human PIK3R3 (phosphoinositide-3-kinase regulatory subunit 3).
WBGene00000002 aat-1 F27C8.1 Amino Acid Transporter aat-1 encodes an amino acid transporter catalytic subunit; when co-expressed in Xenopus oocytes with the ATG-2 glycoprotein subunit, AAT-1 is able to facilitate amino acid uptake and exchange, showing a relatively high affinity for small and some large neutral amino acids; in addition, AAT-1 is able to covalently associate with ATG-2 or ATG-1 to form heterodimers in the Xenopus expression system; when co-expressed with ATG-2, AAT-1 localizes to the cell surface of oocytes, but when expressed alone or with ATG-1, AAT-1 localizes intracellularly. Contributes to L-amino acid transmembrane transporter activity. Involved in amino acid transmembrane transport. Located in plasma membrane. Part of amino acid transport complex. Expressed in egg-laying apparatus; head motor neurons; and tail. Human ortholog(s) of this gene implicated in cystinuria and lysinuric protein intolerance. Is an ortholog of human SLC7A8 (solute carrier family 7 member 8).
WBGene00000003 aat-2 F07C3.7 Amino Acid Transporter aat-2 encodes a predicted amino acid transporter catalytic subunit; when co-expressed in Xenopus oocytes with a glycoprotein subunit, however, AAT-2 is not able to induce amino acid uptake. Predicted to enable L-amino acid transmembrane transporter activity. Predicted to be involved in L-alpha-amino acid transmembrane transport and L-amino acid transport. Predicted to be located in membrane. Predicted to be integral component of membrane. Human ortholog(s) of this gene implicated in cystinuria. Is an ortholog of human SLC7A8 (solute carrier family 7 member 8).
CodePudding user response：
I'm not sure whether I understand your question right. But to achieve the result in your data frame picture I'd suggest something like
awk '
BEGIN { COLSEP = "\t"; gcd = ""; ad = ""; cd = ""; flag = 0 }
/^WBGene/ { printf "\n%s%s%s%s%s", $1, COLSEP, $2, COLSEP, $3 }
/^Gene class description:/ { flag = 1; $1=$2=$3=""; }
/^Automated description:/ { flag = 2; $1=$2=""; }
/^Concise description:/ { flag = 3; $1=$2=""; }
/=/ { flag = 0; printf "%s%s%s%s%s", gcd, COLSEP, cd, COLSEP, ad; gcd = ""; ad = ""; cd = ""}
flag==1 { gcd = gcd $0 }
flag==2 { ad = ad $0 }
flag==3 { cd = cd $0 }
' c_elegans.PRJNA13758.WS283.functional_descriptions.txt