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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)						    BSD General Commands Manual 						  SPLIT(1)

NAME
split -- split a file into pieces SYNOPSIS
split [-a suffix_length] [-b byte_count[k|m]] [-l line_count] [-p pattern] [file [name]] DESCRIPTION
The split utility reads the given file and breaks it up into files of 1000 lines each. If file is a single dash ('-') or absent, split reads from the standard input. The options are as follows: -a Use suffix_length letters to form the suffix of the file name. -b Create smaller files byte_count bytes in length. If ``k'' is appended to the number, the file is split into byte_count kilobyte pieces. If ``m'' is appended to the number, the file is split into byte_count megabyte pieces. -l Create smaller files n lines in length. -p pattern The file is split whenever an input line matches pattern, which is interpreted as an extended regular expression. The matching line will be the first line of the next output file. This option is incompatible with the -b and -l options. If additional arguments are specified, the first is used as the name of the input file which is to be split. If a second additional argument is specified, it is used as a prefix for the names of the files into which the file is split. In this case, each file into which the file is split is named by the prefix followed by a lexically ordered suffix using suffix_length characters in the range ``a-z''. If -a is not speci- fied, two letters are used as the suffix. If the name argument is not specified, the file is split into lexically ordered files named with prefixes in the range of ``x-z'' and with suffixes as above. SEE ALSO
csplit(1), re_format(7) STANDARDS
The split utility conforms to IEEE Std 1003.1-2001 (``POSIX.1''). HISTORY
A split command appeared in Version 3 AT&T UNIX. BUGS
For historical reasons, if you specify name, split can only create 676 separate files. The default naming convention allows 2028 separate files. The -a option can be used to work around this limitation. The maximum line length for matching patterns is 65536. BSD
April 16, 1994 BSD
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