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Full Discussion: Bash to append array value to file before copying
Top Forums UNIX for Beginners Questions & Answers Bash to append array value to file before copying Post 303039946 by cmccabe on Friday 18th of October 2019 12:04:05 PM
Old 10-18-2019
Hopefully, this is better and helps:
Code:
# Set run array
array=( $(awk -F '\n' -v RS="" -v ref="$s5" '$0 ~ ref {d=split($0, val, " "); for(i=2;i<d;i+=2) printf "%s ",val[i]; printf "\n"}' list | tr -d '\r') )  ## match run in rna.barcode and extract patient

# iterate through array
for ID in "${array[*]}" ; do
echo "$ID" > /tmp/out.txt
       echo "( cd /path/to/${ID}*/path/to/folder && xec sshpass -f file.txt scp -- *.png* xxx@xxx.xx.xx.xxx:/path/to/destination/${ID}-cn_results)"
       sshpass -f out.txt ssh -o strictHostKeyChecking=no -t xxx@xxx.xx.xx.xx
done

Contents of out --- This is array with all samples one one line ---
Code:
ID1 ID2

echo to terminal
Code:
( cd /path/to/ID1 ID2*/*/path/to/folder && exec sshpass -f file.txt scp -- *.png* xxx@xxx.xx.xx.xxx:/path/to/destination/ID1 ID2-cn_results.png)

Code:
├──/path/to/   ---- common path after ssh ---
│   ├── ID1*   --- unique ${ID}* represents random text ---
│   │   └── /this/ID1/folder
│   ├── ID2*   --- unique ${ID}* represents random text ---
│   │   └── /this/ID2/folder
Description:

After ssh to the common path on the server, each unique ID is used to further navigate to folder. In each folder there is a png (cn_results), that the unique ID is append to (ID-cn_results) and this 
append file is scp to xxx@xxx.xx.xx.xxx:/path/to/destination. It seems that since array is one line both are being used and that is causing the error?

 

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LEARN ABOUT DEBIAN

bio::biblio::medlinearticle

Bio::Biblio::MedlineArticle(3pm)			User Contributed Perl Documentation			  Bio::Biblio::MedlineArticle(3pm)

NAME

       Bio::Biblio::MedlineArticle - Representation of a MEDLINE article

SYNOPSIS

	 $obj = Bio::Biblio::MedlineArticle->new(-mesh_headings =>
						   #array ref of hashes
						);

	 # how are Mesh terms stored:
	 use Data::Dumper;
	 print Data::Dumper->Dump ( [$obj->mesh_headings], ['MeshHeadings']);

	 #It produces (something like) this:
	 #'MeshHeadings' => [
	 #	 { 'descriptorName' => 'Adult' },
	 #	 { 'descriptorName' => 'Cardiovascular Diseases',
	 #	   'subHeadings'    => [ { 'subHeading' => 'etiology' },
	 #				 { 'majorTopic' => 'Y',
	 #				   'subHeading' => 'mortality' } ] },
	 #	 { 'descriptorName' => 'Child Development',
	 #	   'subHeadings'    => [ { 'majorTopic' => 'Y',
	 #				   'subHeading' => 'physiology' } ] },
	 #	 { 'descriptorName' => 'Human' },
	 #	]

DESCRIPTION

       A storage object for a MEDLINE article.	See its place in the class hierarchy in
       http://www.ebi.ac.uk/~senger/openbqs/images/bibobjects_perl.gif

   Attributes
       The following attributes are specific to this class (however, you can also set and get all attributes defined in the parent classes):

	 affiliation
	 chemicals			type: array ref of hashes
	 citation_owner
	 comment_ins			type: array ref of hashes
	 comment_ons			type: array ref of hashes
	 date_of_electronic_publication
	 erratum_fors			type: array ref of hashes
	 erratum_in			type: array ref of hashes
	 gene_symbols
	 general_notes			type: array ref of hashes
	 grant_list_complete
	 grants 			type: array ref of hashes
	 medline_date
	 medline_id
	 medline_page
	 mesh_headings			type: array ref of hashes
	 number_of_references
	 original_report_ins		type: array ref of hashes
	 other_abstracts		type: array ref of hashes
	 other_ids			type: array ref of hashes
	 other_languages
	 pmid
	 republished_froms		type: array ref of hashes
	 republished_ins		type: array ref of hashes
	 retraction_ins 		type: array ref of hashes
	 retraction_ofs 		type: array ref of hashes
	 season
	 status
	 summary_for_patients_ins	type: array ref of hashes
	 update_ins			type: array ref of hashes
	 update_ofs			type: array ref of hashes
	 vernacular_title

SEE ALSO

       o   OpenBQS home page: http://www.ebi.ac.uk/~senger/openbqs/

       o   Comments to the Perl client: http://www.ebi.ac.uk/~senger/openbqs/Client_perl.html

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHORS

       Heikki Lehvaslaiho (heikki-at-bioperl-dot-org), Martin Senger (senger@ebi.ac.uk)

COPYRIGHT

       Copyright (c) 2002 European Bioinformatics Institute. All Rights Reserved.

       This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

DISCLAIMER

       This software is provided "as is" without warranty of any kind.

perl v5.14.2							    2012-03-02					  Bio::Biblio::MedlineArticle(3pm)
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