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Top Forums Shell Programming and Scripting Perl error in batch command but works one at a time Post 302990885 by cmccabe on Thursday 2nd of February 2017 08:47:05 AM
Old 02-02-2017
Perl error in batch command but works one at a time

In the below perl executes if one file is processed perfect. However, when multiple files are processed in batch which is preferred I get the below error that I can not seem to fix it as the '' necessary for the command to execute, but seem to only work for one -arg option. Thank you Smilie.

command to process one file at a time
Code:
perl -ne 'chomp; system ("perl table_annovar.pl -vcfinput file.vcf humandb/ -buildver hg19 -arg '-hgvs',,,,, -remove -protocol IDP.refGene,avsnp147,popfreq_all_20150413,spidex,dbnsfp33a,clinvar_20161128 -operation g,f,f,f,f,f -otherinfo -nastring .")' < target.txt

Using a batch command I get:

Batch command to process all files in target.txt
Code:
perl -ne 'chomp; system ("perl table_annovar.pl -vcfinput $_ humandb/ -buildver hg19 -arg '-splicing_threshold 50 -hgvs',,,,, -remove -protocol IDP.refGene,avsnp147,popfreq_all_20150413,spidex,dbnsfp33a,clinvar_20161128 -operation g,f,f,f,f,f -otherinfo -nastring .")' < target.txt
Can't find string terminator '"' anywhere before EOF at -e line 1.

Code:
perl -ne 'chomp; system ("perl table_annovar.pl -vcfinput $_ humandb/ -buildver hg19 -arg -splicing_threshold 50 -hgvs,,,,, -remove -protocol IDP.refGene,avsnp147,popfreq_all_20150413,spidex,dbnsfp33a,clinvar_20161128 -operation g,f,f,f,f,f -otherinfo -nastring .")' < target.txt
Unknown option: hgvs,,,,,


Last edited by cmccabe; 02-02-2017 at 09:52 AM.. Reason: fixed format, added details
 

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Locale::Codes::LangExt(3)				User Contributed Perl Documentation				 Locale::Codes::LangExt(3)

NAME
Locale::Codes::LangExt - standard codes for language extension identification SYNOPSIS
use Locale::Codes::LangExt; $lext = code2langext('acm'); # $lext gets 'Mesopotamian Arabic' $code = langext2code('Mesopotamian Arabic'); # $code gets 'acm' @codes = all_langext_codes(); @names = all_langext_names(); DESCRIPTION
The "Locale::Codes::LangExt" module provides access to standard codes used for identifying language extensions, such as those as defined in the IANA language registry. Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default IANA language registry codes will be used. SUPPORTED CODE SETS
There are several different code sets you can use for identifying language extensions. A code set may be specified using either a name, or a constant that is automatically exported by this module. For example, the two are equivalent: $lext = code2langext('acm','alpha'); $lext = code2langext('acm',LOCALE_LANGEXT_ALPHA); The codesets currently supported are: alpha This is the set of three-letter (lowercase) codes from the IANA language registry, such as 'acm' for Mesopotamian Arabic. This is the default code set. ROUTINES
code2langext ( CODE [,CODESET] ) langext2code ( NAME [,CODESET] ) langext_code2code ( CODE ,CODESET ,CODESET2 ) all_langext_codes ( [CODESET] ) all_langext_names ( [CODESET] ) Locale::Codes::LangExt::rename_langext ( CODE ,NEW_NAME [,CODESET] ) Locale::Codes::LangExt::add_langext ( CODE ,NAME [,CODESET] ) Locale::Codes::LangExt::delete_langext ( CODE [,CODESET] ) Locale::Codes::LangExt::add_langext_alias ( NAME ,NEW_NAME ) Locale::Codes::LangExt::delete_langext_alias ( NAME ) Locale::Codes::LangExt::rename_langext_code ( CODE ,NEW_CODE [,CODESET] ) Locale::Codes::LangExt::add_langext_code_alias ( CODE ,NEW_CODE [,CODESET] ) Locale::Codes::LangExt::delete_langext_code_alias ( CODE [,CODESET] ) These routines are all documented in the Locale::Codes::API man page. SEE ALSO
Locale::Codes The Locale-Codes distribution. Locale::Codes::API The list of functions supported by this module. http://www.iana.org/assignments/language-subtag-registry The IANA language subtag registry. AUTHOR
See Locale::Codes for full author history. Currently maintained by Sullivan Beck (sbeck@cpan.org). COPYRIGHT
Copyright (c) 2011-2013 Sullivan Beck This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.16.3 2013-02-27 Locale::Codes::LangExt(3)
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