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Top Forums UNIX for Beginners Questions & Answers How to insert a string and variable at specified position in command in bash? Post 303042141 by rbatte1 on Monday 16th of December 2019 09:55:13 AM
Old 12-16-2019
Do you want something more like:
Code:
printf -- "/path/to/xxx.py \\\\\n%s\n\t--ref /path/to/file \\\\\n\t--run /path/to/data\n" \                       # Set up the output format with fixed strings and an assignment for where the data goes
   "$(for bamfile in *.bam; do printf -- "\t\t--bam %s \\\\\n"    "${bamfile}"; done)"                            # Collect & list the data file lines here, tab indenting each with \t and finishing with the formatting to append the \ and the new-line
                                                                                                                  # This will get used in the above line as the input for the data.

Lots of escaping in the strings which makes it look a bit messy, but it seems to work for me. After creating dummy files as you have, I got the output:-
Code:
/path/to/xxx.py \
		--bam s1.bam \
		--bam s2.bam \
		--bam s3.bam \
		--bam s4.bam \
	--ref /path/to/file \
	--run /path/to/data

Does this do what you need?


Robin

Last edited by rbatte1; 12-17-2019 at 07:07 AM..
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Devel::Refcount(3pm)					User Contributed Perl Documentation				      Devel::Refcount(3pm)

NAME
"Devel::Refcount" - obtain the REFCNT value of a referent SYNOPSIS
use Devel::Refcount qw( refcount ); my $anon = []; print "Anon ARRAY $anon has " . refcount($anon) . " reference "; my $otherref = $anon; print "Anon ARRAY $anon now has " . refcount($anon) . " references "; DESCRIPTION
This module provides a single function which obtains the reference count of the object being pointed to by the passed reference value. FUNCTIONS
$count = refcount($ref) Returns the reference count of the object being pointed to by $ref. COMPARISON WITH SvREFCNT This function differs from "Devel::Peek::SvREFCNT" in that SvREFCNT() gives the reference count of the SV object itself that it is passed, whereas refcount() gives the count of the object being pointed to. This allows it to give the count of any referent (i.e. ARRAY, HASH, CODE, GLOB and Regexp types) as well. Consider the following example program: use Devel::Peek qw( SvREFCNT ); use Devel::Refcount qw( refcount ); sub printcount { my $name = shift; printf "%30s has SvREFCNT=%d, refcount=%d ", $name, SvREFCNT($_[0]), refcount($_[0]); } my $var = []; printcount 'Initially, $var', $var; my $othervar = $var; printcount 'Before CODE ref, $var', $var; printcount '$othervar', $othervar; my $code = sub { undef $var }; printcount 'After CODE ref, $var', $var; printcount '$othervar', $othervar; This produces the output Initially, $var has SvREFCNT=1, refcount=1 Before CODE ref, $var has SvREFCNT=1, refcount=2 $othervar has SvREFCNT=1, refcount=2 After CODE ref, $var has SvREFCNT=2, refcount=2 $othervar has SvREFCNT=1, refcount=2 Here, we see that SvREFCNT() counts the number of references to the SV object passed in as the scalar value - the $var or $othervar respectively, whereas refcount() counts the number of reference values that point to the referent object - the anonymous ARRAY in this case. Before the CODE reference is constructed, both $var and $othervar have SvREFCNT() of 1, as they exist only in the current lexical pad. The anonymous ARRAY has a refcount() of 2, because both $var and $othervar store a reference to it. After the CODE reference is constructed, the $var variable now has an SvREFCNT() of 2, because it also appears in the lexical pad for the new anonymous CODE block. PURE-PERL FALLBACK An XS implementation of this function is provided, and is used by default. If the XS library cannot be loaded, a fallback implementation in pure perl using the "B" module is used instead. This will behave identically, but is much slower. Rate pp xs pp 225985/s -- -66% xs 669570/s 196% -- SEE ALSO
o Test::Refcount - assert reference counts on objects AUTHOR
Paul Evans <leonerd@leonerd.org.uk> perl v5.14.2 2011-11-15 Devel::Refcount(3pm)
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