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Top Forums UNIX for Beginners Questions & Answers awk script to extract transcript information from gff3 file Post 303043936 by rdrtx1 on Tuesday 11th of February 2020 10:11:15 AM
Old 02-11-2020
Code:
awk '
(! h++) {print "transcript_id", "gene_name", "description", "chromosome", "strand", "transcript_start", "transcript_end", "gene_start", "gene_end";}
$9 ~ /ID=.*Name=/ {split($9,a,";");split(a[2], b,"="); gs[b[2]]=$4; ge[b[2]]=$5;}
$3~/.RNA/ {
split($9,a,";");
split(a[2],b,"=");
split(a[5],c,"=");
print b[2], c[2], "Desc", $1, $7, $4, $5, gs[c[2]], ge[c[2]];
}
' OFS="\t" input


Last edited by RavinderSingh13; 02-28-2020 at 01:49 AM..
This User Gave Thanks to rdrtx1 For This Post:
 

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split(1)							   User Commands							  split(1)

NAME
split - split a file into pieces SYNOPSIS
split [-linecount | -l linecount] [-a suffixlength] [file [name]] split [-b n | nk | nm] [-a suffixlength] [file [name]] DESCRIPTION
The split utility reads file and writes it in linecount-line pieces into a set of output-files. The name of the first output-file is name with aa appended, and so on lexicographically, up to zz (a maximum of 676 files). The maximum length of name is 2 characters less than the maximum filename length allowed by the filesystem. See statvfs(2). If no output name is given, x is used as the default (output-files will be called xaa, xab, and so forth). OPTIONS
The following options are supported: -linecount | -l linecount Number of lines in each piece. Defaults to 1000 lines. -a suffixlength Uses suffixlength letters to form the suffix portion of the filenames of the split file. If -a is not specified, the default suffix length is 2. If the sum of the name operand and the suffixlength option-argument would create a filename exceeding NAME_MAX bytes, an error will result; split will exit with a diagnostic message and no files will be created. -b n Splits a file into pieces n bytes in size. -b nk Splits a file into pieces n*1024 bytes in size. -b nm Splits a file into pieces n*1048576 bytes in size. OPERANDS
The following operands are supported: file The path name of the ordinary file to be split. If no input file is given or file is -, the standard input will be used. name The prefix to be used for each of the files resulting from the split operation. If no name argument is given, x will be used as the prefix of the output files. The combined length of the basename of prefix and suffixlength cannot exceed NAME_MAX bytes. See OPTIONS. USAGE
See largefile(5) for the description of the behavior of split when encountering files greater than or equal to 2 Gbyte ( 2^31 bytes). ENVIRONMENT VARIABLES
See environ(5) for descriptions of the following environment variables that affect the execution of split: LANG, LC_ALL, LC_CTYPE, LC_MES- SAGES, and NLSPATH. EXIT STATUS
The following exit values are returned: 0 Successful completion. >0 An error occurred. ATTRIBUTES
See attributes(5) for descriptions of the following attributes: +-----------------------------+-----------------------------+ | ATTRIBUTE TYPE | ATTRIBUTE VALUE | +-----------------------------+-----------------------------+ |Availability |SUNWesu | +-----------------------------+-----------------------------+ |CSI |Enabled | +-----------------------------+-----------------------------+ |Interface Stability |Committed | +-----------------------------+-----------------------------+ |Standard |See standards(5). | +-----------------------------+-----------------------------+ SEE ALSO
csplit(1), statvfs(2), attributes(5), environ(5), largefile(5), standards(5) SunOS 5.11 16 Apr 1999 split(1)
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