I am just not seeing what my problem is here:
FILE
Y 555381 555382 256191 . A AGCCCCCCGCGC . ALLELEID 257892 CLNDISDB MedGen CN169374 CLNDN not_specified CLNHGVS NC_000024.9 !g.555387_555397dupCCCGCGCGCCC CLNREVSTAT criteria_provided,_single_submitter CLINSIG %Likely_benign CLNVC Duplication CLNVCSO SO 1000035 GENEINFO @SHOX
X 585120 585121 265992 . C G . ALLELEID 260809 CLNDISDB MedGen C1845118,OMIM 300582,Orphanet ORPHA314795 CLNDN Short_stature,_idiopathic,_X-linked CLNHGVS NC_000023.10 !g.585121C>G CLNREVSTAT no_assertion_criteria_provided CLINSIG %Likely_benign CLNVC single_nucleotide_variant CLNVCSO SO 0001483 GENEINFO @SHOX
COMMAND & SYNTAX ERROR
awk -F '\t' '{for(i=1 i < NF;i++ && j=1 j < NF;j++ && k=1 k < NF;k++) if($i ~ /@/ && $j ~ /!/ && $k ~ /%/) {print $i"\011"$j"\011"$k}}' FILE > OUTPUT
awk: cmd. line:1: {for(i=1 i < NF;i++ && j=1 j < NF;j++ && k=1 k < NF;k++) if($i ~ /@/ && $j ~ /!/ && $k ~ /%/) {print $i"\011"$j"\011"$k}}
awk: cmd. line:1: ^ syntax error
awk: cmd. line:1: {for(i=1 i < NF;i++ && j=1 j < NF;j++ && k=1 k < NF;k++) if($i ~ /@/ && $j ~ /!/ && $k ~ /%/) {print $i"\011"$j"\011"$k}}
awk: cmd. line:1:
^ syntax error
The interpreter is not liking the semi-colon between NF;k++ and the subsequent closed parenthesis ). Aide appreciated.
1 answer
Given the tab-delimited file in.txt:
Y 555381 555382 256191 . A AGCCCCCCGCGC . ALLELEID 257892 CLNDISDB MedGen CN169374 CLNDN not_specified CLNHGVS NC_000024.9 !g.555387_555397dupCCCGCGCGCCC CLNREVSTAT criteria_provided,_single_submitter CLINSIG %Likely_benign CLNVC Duplication CLNVCSO SO 1000035 GENEINFO @SHOX
X 585120 585121 265992 . C G . ALLELEID 260809 CLNDISDB MedGen C1845118,OMIM 300582,Orphanet ORPHA314795 CLNDN Short_stature,_idiopathic,_X-linked CLNHGVS NC_000023.10 !g.585121C>G CLNREVSTAT no_assertion_criteria_provided CLINSIG %Likely_benign CLNVC single_nucleotide_variant CLNVCSO SO 0001483 GENEINFO @SHOX
You could just look for fields that start with your characters of interest (!, %, and @), print out a tab-delimited line of those fields, and then strip the trailing tab:
$ awk -F'\t' '{ for(i = 1; i <= NF; i++) { if ($i ~ /^[!%@]/) { printf("%s\t", $i); } } printf("\n"); }' in.txt | awk '{ sub(/\t$/, "", $0); print $0; }' > out.txt
The output file out.txt:
$ cat out.txt
!g.555387_555397dupCCCGCGCGCCC %Likely_benign @SHOX
!g.585121C>G %Likely_benign @SHOX
Use cat -te to sanity-check output, so that you can be sure that it has the delimiters and line-ending characters that you need.
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for loopin awk is defined in the manual ( https://www.gnu.org/software/gawk/manual/html_node/For-Statement.html ) as:where are those 3 parts in your code ?
initialization: set i, j, k counters one for each of the desired word prefixes, condition: select the word prefixes @, ! and % and print them out. Go to the next line until the file is exhausted. No?
no. And awk doesn't support multi initialization in the for loop. https://www.gnu.org/software/gawk/manual/html_node/For-Statement.html
OK, back to drawing board. Thanks.
You have four subsections in your
forloop definition, which only allows three. You are getting a syntax error on the third semi-colon. Remove the unnecessary section.Alex, it just hangs when I do this..., Pierre is right, I need another approach.
I am having difficulty understanding what this is trying to do.
Can you show what your expected output should look like, in comparison with the input?
Pairing a single line of input with the expected output would be useful.
Hi! Here is the hoped for output from the FILE given above:
Thanks, this is a beautiful thing. I would be happy to discuss the one time I did this with you privately.
Hello bgold04,
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