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Full Discussion: Check whether a given file is in ASCII format and data is tab-delimited
Top Forums Shell Programming and Scripting Check whether a given file is in ASCII format and data is tab-delimited Post 302115553 by Mandab on Wednesday 25th of April 2007 12:24:15 PM
Old 04-25-2007
Check whether a given file is in ASCII format and data is tab-delimited
Hi All,

Please help me out with a script which checks whether a given file say abc.txt is in ASCII format and data is tab-delimited. If the condition doesn't satisfy then it should generate error code "100" for file not in ASCII format and "105" if it is not in tab-delimited format.
If the above condition satisfies it should check whether field 1 datatype and length(numeric(9)) are same or not. If not error "101" and field 2, field 3 and field 5 (which are of date data type) have data in date format or not. If the data is not in date format(yyyymmdd) or null, then it should generate an error code 112 if field 2 is not in date format or null and 113 if field 3 is not in date format or null etc., If the field is null then it should generate an error code say 150.

Data starts from 2nd line as first line contains filename,filesize and record count.

sample file: abc.txt
row 1 : abc.txt0824673850572854
row 2 : 545689512<tab>20070424<tab>20070414<tab>456.25<tab>20061121<tab>pqr
row 3 : 602584561<tab>20060726<tab>20060524<tab>800.12<tab><tab>abc
row 4 : 24<tab><tab>05242006<tab>22.15<tab>20050815<tab>xyz
.
.
.
row n : 57<tab>20040425<tab>20041214<tab>486.75<tab>20040628<tab>stv
 

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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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