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Top Forums UNIX for Beginners Questions & Answers awk script to extract transcript information from gff3 file Post 303043918 by Maduranga on Tuesday 11th of February 2020 07:04:06 AM
Old 02-11-2020
I came up with this question but that is not correct.
Code:
awk '{if(g3=="mRNA"){split($9,a,"=");split(a[2],b,";");split(g9,ga,"=");split(ga[2],gb,";");print b[1]"\t"gb[1]"\tDesc\t"$1"\t"$7"\t"g4"\t"g5"\tPAC\tPEP\t"$4"\t"$5};g3=$3;g1=$1;g2=$2;g4=$4;g5=$5;g9=$9}'

 

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split(n)						       Tcl Built-In Commands							  split(n)

__________________________________________________________________________________________________________________________________________________

NAME
split - Split a string into a proper Tcl list SYNOPSIS
split string ?splitChars? _________________________________________________________________ DESCRIPTION
Returns a list created by splitting string at each character that is in the splitChars argument. Each element of the result list will con- sist of the characters from string that lie between instances of the characters in splitChars. Empty list elements will be generated if string contains adjacent characters in splitChars, or if the first or last character of string is in splitChars. If splitChars is an empty string then each character of string becomes a separate element of the result list. SplitChars defaults to the standard white-space char- acters. EXAMPLES
Divide up a USENET group name into its hierarchical components: split "comp.lang.tcl.announce" . -> comp lang tcl announce See how the split command splits on every character in splitChars, which can result in information loss if you are not careful: split "alpha beta gamma" "temp" -> al {ha b} {} {a ga} {} a Extract the list words from a string that is not a well-formed list: split "Example with {unbalanced brace character" -> Example with {unbalanced brace character Split a string into its constituent characters split "Hello world" {} -> H e l l o { } w o r l d PARSING RECORD-ORIENTED FILES Parse a Unix /etc/passwd file, which consists of one entry per line, with each line consisting of a colon-separated list of fields: ## Read the file set fid [open /etc/passwd] set content [read $fid] close $fid ## Split into records on newlines set records [split $content " "] ## Iterate over the records foreach rec $records { ## Split into fields on colons set fields [split $rec ":"] ## Assign fields to variables and print some out... lassign $fields userName password uid grp longName homeDir shell puts "$longName uses [file tail $shell] for a login shell" } SEE ALSO
join(n), list(n), string(n) KEYWORDS
list, split, string Tcl split(n)
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