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Full Discussion: Match and retrieve information from file
Top Forums Shell Programming and Scripting Match and retrieve information from file Post 302944275 by Wan Fahmi on Monday 18th of May 2015 11:12:35 AM
Old 05-18-2015
Match and retrieve information from file
Hello

I just want to ask how to get the match of information column 2 file 1 and retrieve information from column 2 file 2. The column exon in file 1 and column color code in file 2.

File 1
Code:
//NODECOLORCODE         "Exon 1"        "ENST00000595813"
//NODECOLORCODE         "Exon 1"        "ENST00000596051"
//NODECOLORCODE         "Exon 2"        "ENST00000243643"
//NODECOLORCODE         "Exon 2"        "ENST00000421033"
//NODECOLORCODE         "Exon 3"        "ENST00000243643"
//NODECOLORCODE         "Exon 3"        "ENST00000421033"
//NODECOLORCODE         "Exon 4"        "ENST00000243643"
//NODECOLORCODE         "Exon 4"        "ENST00000421033"
//NODECOLORCODE         "Exon 5"        "ENST00000421033"
//NODECOLORCODE         "Exon 5"        "ENST00000440291"

File 2
Code:
"Exon 1"        "#FF0000"
"Exon 2"        "#FFD400"
"Exon 3"        "#FFff00"
"Exon 4"        "#2Bff00"
"Exon 5"        "#00ff00"

Desired output

Code:
//NODECOLORCODE         "Exon 1"        "ENST00000595813"        "#FF0000"
//NODECOLORCODE         "Exon 1"        "ENST00000596051"        "#FF0000"
//NODECOLORCODE         "Exon 2"        "ENST00000243643"        "#FFD400"
//NODECOLORCODE         "Exon 2"        "ENST00000421033"        "#FFD400"
//NODECOLORCODE         "Exon 3"        "ENST00000243643"        "#FFff00"
//NODECOLORCODE         "Exon 3"        "ENST00000421033"        "#FFff00"
//NODECOLORCODE         "Exon 4"        "ENST00000243643"        "#2Bff00"
//NODECOLORCODE         "Exon 4"        "ENST00000421033"        "#2Bff00"
//NODECOLORCODE         "Exon 5"        "ENST00000421033"        "#00ff00"
//NODECOLORCODE         "Exon 5"        "ENST00000440291"        "#00ff00"

I try using awk and it doesn't come out with the desired output I want. Thanks

Code:
awk 'FNR==NR {C[$2]=$1;next} FNR==1 {print "NODECLASSCOLOR EXON TRANSCRIPT_ID COLORCODE"; next} $1 in C {print C[$1], $1, $4, $2, $3}'

 

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LEARN ABOUT DEBIAN

asnval

ASNVAL(1)						     NCBI Tools User's Manual							 ASNVAL(1)

NAME

       asnval - validate ASN.1 biological sequence records

SYNOPSIS

       asnval [-] [-A] [-B] [-C N] [-D] [-E str] [-F] [-G] [-J] [-K] [-L filename] [-M] [-N flags] [-P N] [-Q N] [-R N] [-S N] [-T] [-U] [-X] [-Y]
       [-Z] [-a type] [-b] [-c] [-d path] [-e] [-f str] [-i filename] [-k] [-l] [-o filename] [-p path] [-q] [-r] [-u] [-v N] [-x str]

DESCRIPTION

       asnval is a command-line tool to validate ASN.1-format biological sequence records.

OPTIONS

       A summary of options is included below.

       -      Print usage message

       -A     Validate Alignments

       -B     Validate Barcodes

       -C N   Max count

       -D     Disable message suppression

       -E str Only Error Code to Show

       -F     Test network access

       -G     GI lookup from accession

       -J     Require ISO-JTA?

       -K     Summary to error file

       -L filename
	      Log File

       -M     Match locus_tag against General ID

       -N flags
	      Latitude-longitude / country flags
	      0      none
	      1      test state/province
	      2      ignore water exception
	      3      both of the above

       -P N   Highest severity for error to show:
	      0      none
	      1      informational
	      2      warning
	      3      error (default for -Q)
	      4      grounds for rejection (default for -P, -R)

       -Q N   Lowest severity for error to show, per P

       -R N   Severity for error in return code, per P

       -S N   Skip count

       -T     Use Threads

       -U     Genome center submission

       -X     Exon splice check

       -Y     Check against old IDs

       -Z     Remote CDS product fetch

       -a type
	      Input ASN.1 type:
	      a      Automatic (default)
	      c      Catenated
	      z      Any
	      e      seq-Entry
	      b      Bioseq
	      s      bioseq-Set
	      m      seq-subMit
	      t      baTch bioseq-set
	      u      batch seq-sUbmit

       -b     Batch file is Binary

       -c     Batch file is Compressed

       -d path
	      Path to Indexed Binary ASN.1 Data

       -e     Ignore transcription/translation Exceptions

       -x str Substring filter

       -i filename
	      Single input file (standard input by default)

       -k     Local fetching

       -l     Lock components in advance

       -o filename
	      Single output file

       -p path
	      Path to ASN.1 Files

       -q     Taxonomy lookup

       -r     Remote Fetching from ID

       -u     Recurse

       -v N   Verbosity:
	      1      Standard report (default)
	      2      Accession / severity / code (space delimited)
	      3      Accession / severity / code (tab delimited)
	      4      XML report
	      5      Accession / GI / severity / code (tab delimited)

       -x str File selection substring (.ent by default)

AUTHOR

       The National Center for Biotechnology Information.

SEE ALSO

       asndisc(1), cleanasn(1), sequin(1).

NCBI
								    2012-06-24								 ASNVAL(1)
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