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Full Discussion: awk to split one field and print the last two fields within the split part.
Top Forums Shell Programming and Scripting awk to split one field and print the last two fields within the split part. Post 302624773 by yifangt on Monday 16th of April 2012 09:41:57 PM
Old 04-16-2012
awk to split one field and print the last two fields within the split part.
Hello;
I have a file consists of 4 columns separated by tab. The problem is the third fields. Some of the them are very long but can be split by the vertical bar "|". Also some of them do not contain the string "UniProt", but I could ignore it at this moment, and sort the file afterwards. Here is the input file like (>100k rows!!!):
Code:
B_1019927    ES904790    Unknown    Unknown protein
B_1065532    JCVI_27855   JCVI_27855|gb|DW997385|gb|CD815403|gb|EV204160|gb|CD813268|gb|EX038736|UniProt|Q8RWM2    Putative uncharacterized protein At4g36940
B_1065533    JCVI_27856   JCVI_27856|gb|CD826551|gb|DY030639|gb|CX272767|gb|EV056662|gb|EX022554|gb|EX038271|UniProt|Q3E9T4    Protein At4g31430
B_1065534    JCVI_27857   JCVI_27857|gb|DY023794|gb|EE530065|gb|CX280035|UniProt|Q84WF5    Probable VAMP-like protein At1g33475
B_1065535    JCVI_27858   JCVI_27858|gb|ES941909|gb|ES940913|gb|EE514812|UniProt|Q8LBM4    Iron-sulfur assembly protein IscA-like 1, mitochondrial precursor

I want the output file with the truncated field-3, which is like following:
Code:
B_1019927    ES904790    Unknown    Unknown protein
B_1065532    JCVI_27855    UniProt    Q8RWM2     Putative uncharacterized protein At4g36940
B_1065533    JCVI_27856    UniProt    Q3E9T4     Protein At4g31430
B_1065534    JCVI_27857    UniProt    Q84WF5     Probable VAMP-like protein At1g33475
B_1065535    JCVI_27858    Uniprot    Q8LBM4     Iron-sulfur assembly protein IscA-like 1, mitochondrial precursor

What I did is by matching the "UniProt" string in the third field, split this field and only print the last two columns of the split fields, the original 3 fields ($1, $2, $4) need to be printed untouched.

Here is my code:
Code:
awk 'FS="\t" {for(i=1;i<=NF;i++) if(match($i,"UniProt")) split($i, a, "|"); {print $1, "\t", $2, "\t", $a[-2],"\t", $a[-1],"\t",$NF}}' infile.csv

Have struggled for a while, but did not work out. Appreciate your expertise to help me out. Thanks a lot! Yifang
 

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LEARN ABOUT DEBIAN

seqwords

SEQWORDS(1e)						     EMBOSS Manual for Debian						      SEQWORDS(1e)

NAME

       seqwords - Generates DHF files from keyword search of UniProt.

SYNOPSIS

       seqwords -keyfile infile -spfile infile -outfile outfile

       seqwords -help

DESCRIPTION

       seqwords is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Protein:3D
       Structure" command group(s).

OPTIONS

   Input section
       -keyfile infile
	   This option specifies the name of keywords file (input). This contains a list of keywords specific to a number of SCOP or CATH families
	   and superfamilies used by SEQWORDS to search a sequence database.

       -spfile infile
	   This option specifies the name of the sequence database (input) to search.

   Output section
       -outfile outfile
	   This option specifies the name of the DHF file (domain hits file) (output). A 'domain hits file' contains database hits (sequences)
	   with domain classification information, in the DHF format (FASTA-like). The hits are relatives to a SCOP or CATH family (or other node
	   in the structural hierarchies) and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are
	   generated by using SEQSEARCH, hits retrieved by a sparse protein signatare by using SIGSCAN or various types of HMM and profile by
	   using LIBSCAN. Default value: test.hits

BUGS

       Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers
       (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

       seqwords is fully documented via the tfm(1) system.

AUTHOR

       Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
	   Wrote the script used to autogenerate this manual page.

COPYRIGHT

       This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as
       EMBOSS itself.

DOMSEARCH 0.1.0++20100721					    08/11/2010							      SEQWORDS(1e)
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