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Shell Programming and Scripting
awk to add text to each line of matching id
Post 303029014 by cmccabe on Saturday 19th of January 2019 04:24:46 PM
01-19-2019
Quote:
Are the ranges given in your first input file always in increasing numerical order for each $1,$4 set of values (as in your sample file f1)? If they are we can use that information to make your code run faster.
Quote:
Is the fifth subfield of $4 in your second input file always identical to the $1 value on the same input line (as in your sample files)? If they are, we can use that information to make your code run faster.
Quote:
You note that your input files fields are separated by tabs. Do you want the output file to be tab delimited too; or do you want the output to be delimited by spaces as shown in your sample output?
You are correct in that I meant to be looking for inclusive endpoints so the >=/<= is what I should have used.
Quote:
Is it your intent to print the line containing exon if either endpoint is in an entry in the first input file for that $1,$4 pair, or should it only print the exon line if both endpoints are in range?
Thank you very much
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LEARN ABOUT OPENDARWIN
cut
CUT(1) BSD General Commands Manual CUT(1) NAME
cut -- select portions of each line of a file SYNOPSIS
cut -b list [-n] [file ...] cut -c list [file ...] cut -f list [-d delim] [-s] [file ...] DESCRIPTION
The cut utility selects portions of each line (as specified by list) from each file and writes them to the standard output. If no file argu- ments are specified, or a file argument is a single dash ('-'), cut reads from from the standard input. The items specified by list can be in terms of column position or in terms of fields delimited by a special character. Column numbering starts from 1. The list option argument is a comma or whitespace separated set of increasing numbers and/or number ranges. Number ranges consist of a num- ber, a dash ('-'), and a second number and select the fields or columns from the first number to the second, inclusive. Numbers or number ranges may be preceded by a dash, which selects all fields or columns from 1 to the first number. Numbers or number ranges may be followed by a dash, which selects all fields or columns from the last number to the end of the line. Numbers and number ranges may be repeated, over- lapping, and in any order. It is not an error to select fields or columns not present in the input line. The options are as follows: -b list The list specifies byte positions. -c list The list specifies character positions. -d delim Use the first character of delim as the field delimiter character instead of the tab character. -f list The list specifies fields, delimited in the input by a single tab character. Output fields are separated by a single tab character. -n Do not split multi-byte characters. -s Suppress lines with no field delimiter characters. Unless specified, lines with no delimiters are passed through unmodified. ENVIRONMENT
The LANG, LC_ALL and LC_CTYPE environment variables affect the execution of cut if the -n option is specified. Their effect is described in environ(7). EXAMPLES
Extract users' login names and shells from the system passwd(5) file as ``name:shell'' pairs: cut -d : -f 1,7 /etc/passwd Show the names and login times of the currently logged in users: who | cut -c 1-16,26-38 DIAGNOSTICS
The cut utility exits 0 on success, and >0 if an error occurs. SEE ALSO
paste(1) STANDARDS
The cut utility conforms to IEEE Std 1003.2-1992 (``POSIX.2''). HISTORY
A cut command appeared in AT&T System III UNIX. BUGS
The -c option is a synonym for the -b option, which causes incorrect behaviour in locales that support multibyte characters. When operating on fields (-f option is specified), cut does not recognise multibyte characters, and the delim character is recognised in the middle of multibyte sequences. BSD
June 6, 1993 BSD