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Full Discussion: Read multiple text files and copy data to csv
Top Forums Shell Programming and Scripting Read multiple text files and copy data to csv Post 302970009 by RudiC on Thursday 31st of March 2016 08:12:20 AM
Old 03-31-2016
awk allows for quite a long input file list, so try
- adding */file*.txt and further down the tree
- using a command substitution like "$(find . -type f)"

Should system limits like LINE_MAX be exceeded, you need to run the awk script on several split input streams.
Last edited by RudiC; 03-31-2016 at 11:21 AM.. Reason: inserted missing double quote
This User Gave Thanks to RudiC For This Post:
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LEARN ABOUT DEBIAN

csv2mipe

CSV2MIPE(1)						User Contributed Perl Documentation					       CSV2MIPE(1)

NAME

       csv2mipe.pl - Generates MIPE file based on 3 tab-delimited files
	 based on MIPE version v1.1
	 arguments: * tab-delimited file with PCR-level data
		    * tab-delimited file with SNP-level data
		    * tab-delimited file with assay-level data

	 Columns in file with PCR-level data:
	   pcr_id
	   pcr_modified (might be multiple, divided by semi-colon ";")
	   pcr_project (might be multiple, divided by semi-colon ";")
	   pcr_researcher (might be multiple, divided by semi-colon ";")
	   pcr_species
	   source_type
	   source_id
	   design_seq
	   primer1_oligo
	   primer1_seq
	   primer1_tm
	   primer2_oligo
	   primer2_seq
	   primer2_tm
	   design_remark (might be multiple, divided by semi-colon ";")
	   use_seq
	   use_revcomp
	   use_remark (might be multiple, divided by semi-colon ";")
	   pcr_remark (might be multiple, divided by semi-colon ";")

	 Columns in file with SNP-level data:
	   pcr_id
	   snp_id
	   snp_pos
	   snp_amb
	   snp_remark (might be multiple, divided by semi-colon ";")

	 Columns in file with assay-level data:
	   pcr_id
	   snp_id
	   assay_id
	   assay_type
	   assay_enzyme
	   assay_oligo
	   assay_specific
	   assay_tail
	   assay_strand
	   assay_remark (might be multiple, divided by semi-colon ";")

SYNOPSIS

       csv2mipe.pl <pcr_file.csv> <snp_file.csv> <assay_file.csv>

ADDITIONAL INFO

       See http://mipe.sourceforge.net

AUTHOR

       Jan Aerts (jan.aerts@bbsrc.ac.uk)

perl v5.14.2							    2005-07-20							       CSV2MIPE(1)
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