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

NAME
Locale::Codes::LangFam - standard codes for language extension identification SYNOPSIS
use Locale::Codes::LangFam; $lext = code2langfam('apa'); # $lext gets 'Apache languages' $code = langfam2code('Apache languages'); # $code gets 'apa' @codes = all_langfam_codes(); @names = all_langfam_names(); DESCRIPTION
The "Locale::Codes::LangFam" module provides access to standard codes used for identifying language families, such as those as defined in ISO 639-5. Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default ISO 639-5 language family codes will be used. SUPPORTED CODE SETS
There are several different code sets you can use for identifying language families. 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 = code2langfam('apa','alpha'); $lext = code2langfam('apa',LOCALE_LANGFAM_ALPHA); The codesets currently supported are: alpha This is the set of three-letter (lowercase) codes from ISO 639-5 such as 'apa' for Apache languages. This is the default code set. ROUTINES
code2langfam ( CODE [,CODESET] ) langfam2code ( NAME [,CODESET] ) langfam_code2code ( CODE ,CODESET ,CODESET2 ) all_langfam_codes ( [CODESET] ) all_langfam_names ( [CODESET] ) Locale::Codes::LangFam::rename_langfam ( CODE ,NEW_NAME [,CODESET] ) Locale::Codes::LangFam::add_langfam ( CODE ,NAME [,CODESET] ) Locale::Codes::LangFam::delete_langfam ( CODE [,CODESET] ) Locale::Codes::LangFam::add_langfam_alias ( NAME ,NEW_NAME ) Locale::Codes::LangFam::delete_langfam_alias ( NAME ) Locale::Codes::LangFam::rename_langfam_code ( CODE ,NEW_CODE [,CODESET] ) Locale::Codes::LangFam::add_langfam_code_alias ( CODE ,NEW_CODE [,CODESET] ) Locale::Codes::LangFam::delete_langfam_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.loc.gov/standards/iso639-5/id.php ISO 639-5 . 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::LangFam(3)
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