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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 303042117 by RudiC on Sunday 15th of December 2019 10:34:29 AM
Old 12-15-2019
Not sure I fully understand, and your "Tried" block seems to be gobbledigook, but how about
Code:
while IFS="" read -r LN
  do    [ "$LN" = "${LN##*id}" ] && echo "$LN" || for FN in *.bam
                                                    do echo "     -- bam $FN \\"
                                                    done
  done < file
/path/to/xxx.py \
     -- bam s1.bam \
     -- bam s2.bam \
     -- bam s3.bam \
     -- bam s4.bam \
     --ref /path/to/file \
     --run /ptah/to/data


EDIT: or
Code:
ls *.bam | awk 'NR == FNR {T = T DL "     --bam " $0 " \\"; DL = RS; next} /id/ {print T; next} 1' - file


Last edited by RudiC; 12-15-2019 at 11:52 AM..
This User Gave Thanks to RudiC For This Post:
 

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Config::BaseConfigurator(3pm)				User Contributed Perl Documentation			     Config::BaseConfigurator(3pm)

NAME
Log::Log4perl::Config::BaseConfigurator - Configurator Base Class SYNOPSIS
This is a virtual base class, all configurators should be derived from it. DESCRIPTION
METHODS "new" Constructor, typically called like my $config_parser = SomeConfigParser->new( file => $file, ); my $data = $config_parser->parse(); Instead of "file", the derived class "SomeConfigParser" may define any type of configuration input medium (e.g. "url => 'http://foobar'"). It just has to make sure its "parse()" method will later pull the input data from the medium specified. The base class accepts a filename or a reference to an array of text lines: "file" Specifies a file which the "parse()" method later parses. "text" Specifies a reference to an array of scalars, representing configuration records (typically lines of a file). Also accepts a simple scalar, which it splits at its newlines and transforms it into an array: my $config_parser = MyYAMLParser->new( text => ['foo: bar', 'baz: bam', ], ); my $data = $config_parser->parse(); If either "file" or "text" parameters have been specified in the constructor call, a later call to the configurator's "text()" method will return a reference to an array of configuration text lines. This will typically be used by the "parse()" method to process the input. "parse" Virtual method, needs to be defined by the derived class. Parser requirements o If the parser provides variable substitution functionality, it has to implement it. o The parser's "parse()" method returns a reference to a hash of hashes (HoH). The top-most hash contains the top-level keywords ("category", "appender") as keys, associated with values which are references to more deeply nested hashes. o The "log4perl." prefix (e.g. as used in the PropertyConfigurator class) is stripped, it's not part in the HoH structure. o Each Log4perl config value is indicated by the "value" key, as in $data->{category}->{Bar}->{Twix}->{value} = "WARN, Logfile" EXAMPLES The following Log::Log4perl configuration: log4perl.category.Bar.Twix = WARN, Screen log4perl.appender.Screen = Log::Log4perl::Appender::File log4perl.appender.Screen.filename = test.log log4perl.appender.Screen.layout = Log::Log4perl::Layout::SimpleLayout needs to be transformed by the parser's "parse()" method into this data structure: { appender => { Screen => { layout => { value => "Log::Log4perl::Layout::SimpleLayout" }, value => "Log::Log4perl::Appender::Screen", }, }, category => { Bar => { Twix => { value => "WARN, Screen" } } } } For a full-fledged example, check out the sample YAML parser implementation in "eg/yamlparser". It uses a simple YAML syntax to specify the Log4perl configuration to illustrate the concept. SEE ALSO
Log::Log4perl::Config::PropertyConfigurator Log::Log4perl::Config::DOMConfigurator Log::Log4perl::Config::LDAPConfigurator (tbd!) COPYRIGHT AND LICENSE
Copyright 2002-2009 by Mike Schilli <m@perlmeister.com> and Kevin Goess <cpan@goess.org>. This library is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.10.1 2010-07-21 Config::BaseConfigurator(3pm)
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