lindenb / Verticalize
Licence: mit
Simple tool to verticalize text delimited files.
Stars: ✭ 32
Programming Languages
c
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Verticalize
Simple tool to verticalize text delimited files.
Author: Pierre Lindenbaum Phd @yokofakun
Compilation
make
Usage
verticalize (options) (file|stdin)
Options
- -n first line is NOT the header
- -d (char) delimiter (default: tab)
- -h get help.
Example
Example 1: git log
$ git log --pretty=format:'%h|%an|%s' | verticalize -n -d '|'
>>> 1
$1 : 53c8167
$2 : Pierre Lindenbaum
$3 : 1st
<<< 1
>>> 2
$1 : 9e23c0c
$2 : Pierre Lindenbaum
$3 : Initial commit
<<< 2
Example 2 : A VCF file
$ curl "https://raw.githubusercontent.com/ekg/vcflib/master/samples/sample.vcf" |\
grep -vE "^##" |\
verticalize
>>> 2
$1 #CHROM : 19
$2 POS : 111
$3 ID : .
$4 REF : A
$5 ALT : C
$6 QUAL : 9.6
$7 FILTER : .
$8 INFO : .
$9 FORMAT : GT:HQ
$10 NA00001 : 0|0:10,10
$11 NA00002 : 0|0:10,10
$12 NA00003 : 0/1:3,3
<<< 2
>>> 3
$1 #CHROM : 19
$2 POS : 112
$3 ID : .
$4 REF : A
$5 ALT : G
$6 QUAL : 10
$7 FILTER : .
$8 INFO : .
$9 FORMAT : GT:HQ
$10 NA00001 : 0|0:10,10
$11 NA00002 : 0|0:10,10
$12 NA00003 : 0/1:3,3
<<< 3
>>> 4
$1 #CHROM : 20
$2 POS : 14370
$3 ID : rs6054257
$4 REF : G
$5 ALT : A
$6 QUAL : 29
$7 FILTER : PASS
$8 INFO : NS=3;DP=14;AF=0.5;DB;H2
$9 FORMAT : GT:GQ:DP:HQ
$10 NA00001 : 0|0:48:1:51,51
$11 NA00002 : 1|0:48:8:51,51
$12 NA00003 : 1/1:43:5:.,.
<<< 4
>>> 5
$1 #CHROM : 20
$2 POS : 17330
$3 ID : .
$4 REF : T
$5 ALT : A
$6 QUAL : 3
$7 FILTER : q10
$8 INFO : NS=3;DP=11;AF=0.017
$9 FORMAT : GT:GQ:DP:HQ
$10 NA00001 : 0|0:49:3:58,50
$11 NA00002 : 0|1:3:5:65,3
$12 NA00003 : 0/0:41:3:.,.
<<< 5
>>> 6
$1 #CHROM : 20
$2 POS : 1110696
$3 ID : rs6040355
$4 REF : A
$5 ALT : G,T
$6 QUAL : 67
$7 FILTER : PASS
$8 INFO : NS=2;DP=10;AF=0.333,0.667;AA=T;DB
$9 FORMAT : GT:GQ:DP:HQ
$10 NA00001 : 1|2:21:6:23,27
$11 NA00002 : 2|1:2:0:18,2
$12 NA00003 : 2/2:35:4:.,.
<<< 6
>>> 7
$1 #CHROM : 20
$2 POS : 1230237
$3 ID : .
$4 REF : T
$5 ALT : .
$6 QUAL : 47
$7 FILTER : PASS
$8 INFO : NS=3;DP=13;AA=T
$9 FORMAT : GT:GQ:DP:HQ
$10 NA00001 : 0|0:54:.:56,60
$11 NA00002 : 0|0:48:4:51,51
$12 NA00003 : 0/0:61:2:.,.
<<< 7
>>> 8
$1 #CHROM : 20
$2 POS : 1234567
$3 ID : microsat1
$4 REF : G
$5 ALT : GA,GAC
$6 QUAL : 50
$7 FILTER : PASS
$8 INFO : NS=3;DP=9;AA=G;AN=6;AC=3,1
$9 FORMAT : GT:GQ:DP
$10 NA00001 : 0/1:.:4
$11 NA00002 : 0/2:17:2
$12 NA00003 : 1/1:40:3
<<< 8
>>> 9
$1 #CHROM : 20
$2 POS : 1235237
$3 ID : .
$4 REF : T
$5 ALT : .
$6 QUAL : .
$7 FILTER : .
$8 INFO : .
$9 FORMAT : GT
$10 NA00001 : 0/0
$11 NA00002 : 0|0
$12 NA00003 : ./.
<<< 9
>>> 10
$1 #CHROM : X
$2 POS : 10
$3 ID : rsTest
$4 REF : AC
$5 ALT : A,ATG
$6 QUAL : 10
$7 FILTER : PASS
$8 INFO : .
$9 FORMAT : GT
$10 NA00001 : 0
$11 NA00002 : 0/1
$12 NA00003 : 0|2
<<< 10
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