changing the field values conditionally
Clash Royale CLAN TAG#URR8PPP
up vote
-3
down vote
favorite
#CHROM POS REF ALT PANS_1_1 PANS_1_10 PANS_1_2 PANS_1_5 PANS_1_6 PANS_1_8 PANS_1_9 PANS_200_1 PANS_200_2 PANS_2_1 PANS_2_5 PANS_2_6 PANS_2_7 PANS_2_8 PANS_4_2 PANS_99_11 PANS_99_22 PANS_99_23 PANS_99_24 PANS_99_25 PANS_99_26 PANS_99_27 PANS_99_29 PANS_99_31 PANS_99_32 PANS_99_33 PANS_99_36 PANS_99_4 PANS_99_5 PANS_99_9 PAN_02_2 PNA_02_12 PNA_03_1 PNA_03_2 PNA_03_3 PNA_05_1 PNA_06_1 PNA_06_4 PNA_07_1 PNA_07_10 PNA_07_13 PNA_07_14 PNA_07_22 PNA_07_5 PNA_07_7 PNA_08_1 PNA_11_1 PNA_13_1 PNA_14_2 PNA_15_1 PNA_15_2 PNA_15_3 PNA_18_1 PNA_18_10 PNA_18_10S PNA_18_2 PNA_18_3S PNA_18_5 PNA_18_5S PNA_18_6S PNA_18_7S PNA_18_8S PNA_18_9S PNA_200_1 PNA_200_10 PNA_200_11 PNA_200_12 PNA_200_13 PNA_200_3 PNA_200_5 PNA_200_7 PNA_200_8 PNA_92_7 PNA_97_11 PNA_97_2 PNA_97_3 PNA_97_8 PNA_98_1 PNA_98_11 PNA_98_12 PNA_98_2 PNA_98_3 PNA_98_7 PNA_98_8 PNA_99_1 PNA_99_14 PNA_99_2 PNA_99_3 PNA_99_6 PNA_99_7 PNA_99_8 PNA_99_9
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CP001875.2 904 G A 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0
Need to use awk to convert the allele calls in col 5 onwards
- 0/0 to the ref value in col 3
- 1/1 to the alt value in col 4
- 2/2 to the alt vlaue in col 4 after ,
awk
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#CHROM POS REF ALT PANS_1_1 PANS_1_10 PANS_1_2 PANS_1_5 PANS_1_6 PANS_1_8 PANS_1_9 PANS_200_1 PANS_200_2 PANS_2_1 PANS_2_5 PANS_2_6 PANS_2_7 PANS_2_8 PANS_4_2 PANS_99_11 PANS_99_22 PANS_99_23 PANS_99_24 PANS_99_25 PANS_99_26 PANS_99_27 PANS_99_29 PANS_99_31 PANS_99_32 PANS_99_33 PANS_99_36 PANS_99_4 PANS_99_5 PANS_99_9 PAN_02_2 PNA_02_12 PNA_03_1 PNA_03_2 PNA_03_3 PNA_05_1 PNA_06_1 PNA_06_4 PNA_07_1 PNA_07_10 PNA_07_13 PNA_07_14 PNA_07_22 PNA_07_5 PNA_07_7 PNA_08_1 PNA_11_1 PNA_13_1 PNA_14_2 PNA_15_1 PNA_15_2 PNA_15_3 PNA_18_1 PNA_18_10 PNA_18_10S PNA_18_2 PNA_18_3S PNA_18_5 PNA_18_5S PNA_18_6S PNA_18_7S PNA_18_8S PNA_18_9S PNA_200_1 PNA_200_10 PNA_200_11 PNA_200_12 PNA_200_13 PNA_200_3 PNA_200_5 PNA_200_7 PNA_200_8 PNA_92_7 PNA_97_11 PNA_97_2 PNA_97_3 PNA_97_8 PNA_98_1 PNA_98_11 PNA_98_12 PNA_98_2 PNA_98_3 PNA_98_7 PNA_98_8 PNA_99_1 PNA_99_14 PNA_99_2 PNA_99_3 PNA_99_6 PNA_99_7 PNA_99_8 PNA_99_9
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Need to use awk to convert the allele calls in col 5 onwards
- 0/0 to the ref value in col 3
- 1/1 to the alt value in col 4
- 2/2 to the alt vlaue in col 4 after ,
awk
New contributor
1
What do you have so far? Where are you stuck?
â glenn jackman
1 hour ago
Are you aware of the Bioinformatics StackExchange site? They too are not a script writing service.
â Kusalananda
1 hour ago
You will need thesplit
function and afor
loop with anif / else if / else if
statement in it.
â glenn jackman
1 hour ago
Gavin, please read unix.stackexchange.com/help/how-to-ask and come back to edit your question.
â glenn jackman
1 hour ago
I am thinking something: awk 'split ($4, myArray, ",") {if ($5 ~ "0/0") print $3 else if ($3 ~ "1/1") print $4 else if ($3 ~ "2/2") print ,$4 input_file
â Gavin
23 mins ago
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#CHROM POS REF ALT PANS_1_1 PANS_1_10 PANS_1_2 PANS_1_5 PANS_1_6 PANS_1_8 PANS_1_9 PANS_200_1 PANS_200_2 PANS_2_1 PANS_2_5 PANS_2_6 PANS_2_7 PANS_2_8 PANS_4_2 PANS_99_11 PANS_99_22 PANS_99_23 PANS_99_24 PANS_99_25 PANS_99_26 PANS_99_27 PANS_99_29 PANS_99_31 PANS_99_32 PANS_99_33 PANS_99_36 PANS_99_4 PANS_99_5 PANS_99_9 PAN_02_2 PNA_02_12 PNA_03_1 PNA_03_2 PNA_03_3 PNA_05_1 PNA_06_1 PNA_06_4 PNA_07_1 PNA_07_10 PNA_07_13 PNA_07_14 PNA_07_22 PNA_07_5 PNA_07_7 PNA_08_1 PNA_11_1 PNA_13_1 PNA_14_2 PNA_15_1 PNA_15_2 PNA_15_3 PNA_18_1 PNA_18_10 PNA_18_10S PNA_18_2 PNA_18_3S PNA_18_5 PNA_18_5S PNA_18_6S PNA_18_7S PNA_18_8S PNA_18_9S PNA_200_1 PNA_200_10 PNA_200_11 PNA_200_12 PNA_200_13 PNA_200_3 PNA_200_5 PNA_200_7 PNA_200_8 PNA_92_7 PNA_97_11 PNA_97_2 PNA_97_3 PNA_97_8 PNA_98_1 PNA_98_11 PNA_98_12 PNA_98_2 PNA_98_3 PNA_98_7 PNA_98_8 PNA_99_1 PNA_99_14 PNA_99_2 PNA_99_3 PNA_99_6 PNA_99_7 PNA_99_8 PNA_99_9
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CP001875.2 904 G A 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 1/1 0/0 1/1 0/0 0/0 0/0 0/0 0/0 0/0 ./. 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0 0/0
Need to use awk to convert the allele calls in col 5 onwards
- 0/0 to the ref value in col 3
- 1/1 to the alt value in col 4
- 2/2 to the alt vlaue in col 4 after ,
awk
New contributor
#CHROM POS REF ALT PANS_1_1 PANS_1_10 PANS_1_2 PANS_1_5 PANS_1_6 PANS_1_8 PANS_1_9 PANS_200_1 PANS_200_2 PANS_2_1 PANS_2_5 PANS_2_6 PANS_2_7 PANS_2_8 PANS_4_2 PANS_99_11 PANS_99_22 PANS_99_23 PANS_99_24 PANS_99_25 PANS_99_26 PANS_99_27 PANS_99_29 PANS_99_31 PANS_99_32 PANS_99_33 PANS_99_36 PANS_99_4 PANS_99_5 PANS_99_9 PAN_02_2 PNA_02_12 PNA_03_1 PNA_03_2 PNA_03_3 PNA_05_1 PNA_06_1 PNA_06_4 PNA_07_1 PNA_07_10 PNA_07_13 PNA_07_14 PNA_07_22 PNA_07_5 PNA_07_7 PNA_08_1 PNA_11_1 PNA_13_1 PNA_14_2 PNA_15_1 PNA_15_2 PNA_15_3 PNA_18_1 PNA_18_10 PNA_18_10S PNA_18_2 PNA_18_3S PNA_18_5 PNA_18_5S PNA_18_6S PNA_18_7S PNA_18_8S PNA_18_9S PNA_200_1 PNA_200_10 PNA_200_11 PNA_200_12 PNA_200_13 PNA_200_3 PNA_200_5 PNA_200_7 PNA_200_8 PNA_92_7 PNA_97_11 PNA_97_2 PNA_97_3 PNA_97_8 PNA_98_1 PNA_98_11 PNA_98_12 PNA_98_2 PNA_98_3 PNA_98_7 PNA_98_8 PNA_99_1 PNA_99_14 PNA_99_2 PNA_99_3 PNA_99_6 PNA_99_7 PNA_99_8 PNA_99_9
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Need to use awk to convert the allele calls in col 5 onwards
- 0/0 to the ref value in col 3
- 1/1 to the alt value in col 4
- 2/2 to the alt vlaue in col 4 after ,
awk
awk
New contributor
New contributor
edited 4 mins ago
New contributor
asked 1 hour ago
Gavin
12
12
New contributor
New contributor
1
What do you have so far? Where are you stuck?
â glenn jackman
1 hour ago
Are you aware of the Bioinformatics StackExchange site? They too are not a script writing service.
â Kusalananda
1 hour ago
You will need thesplit
function and afor
loop with anif / else if / else if
statement in it.
â glenn jackman
1 hour ago
Gavin, please read unix.stackexchange.com/help/how-to-ask and come back to edit your question.
â glenn jackman
1 hour ago
I am thinking something: awk 'split ($4, myArray, ",") {if ($5 ~ "0/0") print $3 else if ($3 ~ "1/1") print $4 else if ($3 ~ "2/2") print ,$4 input_file
â Gavin
23 mins ago
add a comment |Â
1
What do you have so far? Where are you stuck?
â glenn jackman
1 hour ago
Are you aware of the Bioinformatics StackExchange site? They too are not a script writing service.
â Kusalananda
1 hour ago
You will need thesplit
function and afor
loop with anif / else if / else if
statement in it.
â glenn jackman
1 hour ago
Gavin, please read unix.stackexchange.com/help/how-to-ask and come back to edit your question.
â glenn jackman
1 hour ago
I am thinking something: awk 'split ($4, myArray, ",") {if ($5 ~ "0/0") print $3 else if ($3 ~ "1/1") print $4 else if ($3 ~ "2/2") print ,$4 input_file
â Gavin
23 mins ago
1
1
What do you have so far? Where are you stuck?
â glenn jackman
1 hour ago
What do you have so far? Where are you stuck?
â glenn jackman
1 hour ago
Are you aware of the Bioinformatics StackExchange site? They too are not a script writing service.
â Kusalananda
1 hour ago
Are you aware of the Bioinformatics StackExchange site? They too are not a script writing service.
â Kusalananda
1 hour ago
You will need the
split
function and a for
loop with an if / else if / else if
statement in it.â glenn jackman
1 hour ago
You will need the
split
function and a for
loop with an if / else if / else if
statement in it.â glenn jackman
1 hour ago
Gavin, please read unix.stackexchange.com/help/how-to-ask and come back to edit your question.
â glenn jackman
1 hour ago
Gavin, please read unix.stackexchange.com/help/how-to-ask and come back to edit your question.
â glenn jackman
1 hour ago
I am thinking something: awk 'split ($4, myArray, ",") {if ($5 ~ "0/0") print $3 else if ($3 ~ "1/1") print $4 else if ($3 ~ "2/2") print ,$4 input_file
â Gavin
23 mins ago
I am thinking something: awk 'split ($4, myArray, ",") {if ($5 ~ "0/0") print $3 else if ($3 ~ "1/1") print $4 else if ($3 ~ "2/2") print ,$4 input_file
â Gavin
23 mins ago
add a comment |Â
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Gavin is a new contributor. Be nice, and check out our Code of Conduct.
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Gavin is a new contributor. Be nice, and check out our Code of Conduct.
Gavin is a new contributor. Be nice, and check out our Code of Conduct.
Gavin is a new contributor. Be nice, and check out our Code of Conduct.
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1
What do you have so far? Where are you stuck?
â glenn jackman
1 hour ago
Are you aware of the Bioinformatics StackExchange site? They too are not a script writing service.
â Kusalananda
1 hour ago
You will need the
split
function and afor
loop with anif / else if / else if
statement in it.â glenn jackman
1 hour ago
Gavin, please read unix.stackexchange.com/help/how-to-ask and come back to edit your question.
â glenn jackman
1 hour ago
I am thinking something: awk 'split ($4, myArray, ",") {if ($5 ~ "0/0") print $3 else if ($3 ~ "1/1") print $4 else if ($3 ~ "2/2") print ,$4 input_file
â Gavin
23 mins ago