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Full Discussion: awk to add text to each line of matching id
Top Forums 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
Old 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.
Yes, these should always be sorted like in f1

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.
Yes, this will always be the case if $4 is found as in f1

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?
f1 will always be tab-delimited except for a whitespace after $3 and $4, but the output would be tab-delimited I did and OFS="\t" but I think the whitespaces are making that not work

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?
I used the || statement to make sure the script works as expected but it could be && as both coordinates should lie within the endpoints (trying to think of a situation where its not the case and not coming up with anything).

Thank you very much Smilie.
 

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unexpand

expand(1)						      General Commands Manual							 expand(1)

NAME

       expand, unexpand - expand tabs to spaces, and vice versa

SYNOPSIS

       tablist] [file ...]

       tablist] [file ...]

   Obsolescent:
       tabstop] tabn] [file ...]

DESCRIPTION

       processes  the named files or the standard input and writes to the standard output with tabs changed into spaces.  Backspace characters are
       preserved in the output, and the column count is decreased by one column for tab calculations.  For proper tab calculation, if a multi-col-
       umn  character  is  to be "backspace'd", it should be followed by multiple backspace characters which equal to it's column width.  If a tab
       character is found after the last tab position, it is replaced by a single space.  is useful for preprocessing character files that contain
       tabs (before sorting, looking at specific columns, etc).

       recognizes the following command-line options and arguments:

	      tablist	     specifies	where  to set the tab positions instead of the default tablist can take two forms.  If it is a single num-
			     ber, tabs are set tablist spaces apart.  tablist can also be a blank- or comma-separated list of increasing positions
			     where tabs are to be set.

	      This option is obsolescent and is equivalent to using

	      This option is obsolescent and is equivalent to using

       processes  the  named  files  or  the  standard	input  and writes to the standard output with spaces changed into tabs where possible.	By
       default, only leading spaces and tabs are converted to maximal strings of tabs.	The default tab position is every 8 characters.  Backspace
       characters  are	preserved  into the output, and the column count is decreased by one column for tab calculations.  For proper tab calcula-
       tion, if a multi-column character is to be "backspace'd", it should be followed by multiple backspace characters which equal to it's column
       width.

       recognizes the following command-line options and arguments:

	      Tabs are inserted whenever they would compress the resultant file
			     by replacing two or more spaces before a tab position.

	      tablist	     specifies	the tab positions.  tablist can take two forms.  If it is a single number, tabs are set every tablist spa-
			     ces apart.  If tablist is a blank- or comma-separated list of increasing positions, tabs are set at those	locations.
			     The  option  implies the option.  If the option is not specified, the default is equivalent to specifying except that
			     is not implied for this case.

EXTERNAL INFLUENCES

   Environment Variables
       determines the interpretation of text as single and/or multi-byte characters.

       determines the language in which messages are displayed.

       If or is not specified in the environment or is set to the empty string, the value of is used as a default for each  unspecified  or  empty
       variable.  If is not specified or is set to the empty string, a default of "C" (see lang(5)) is used instead of

       If  any internationalization variable contains an invalid setting, and behave as if all internationalization variables are set to "C".  See
       environ(5).

       If is set to a non-empty string value, it overrides the values of all the other internationalization variables.

   International Code Set Support
       Single- and multi-byte character code sets are supported with the exception that do not recognize multi-byte alternative space characters.

STANDARDS CONFORMANCE

																	 expand(1)
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