sed substitute command -- need help Post: 302777189

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Top Forums Shell Programming and Scripting sed substitute command -- need help Post 302777189 by pathunkathunk on Thursday 7th of March 2013 12:42:01 PM

03-07-2013

Registered User

sed substitute command -- need help

I am trying to do what I thought should be a simple substitution, but I can't get it to work.

File:

Quote:

>m.149837_g.149837__ORF_g.149837_m.149837_type:internal_len:169_(-)_comp100001_c0_seq1:3-509(-)
FHPPVSDSCKRCDMYKNQIKIAPENEKIQLNADHELHLRKAESARNGMNNDVELCKTDPN
KVTVIAFDLMKTLSTPSLSVGVAYYKRQLSTYNLGIHNLTTNDAYMYVWNESMASRGPQE
IGSCLLHFIKNYVHTEQLIMYSDQCGGQNRNIKMALICNFVVGSNDYLP
>m.180533_g.180533__ORF_g.180533_m.180533_type:internal_len:99_(-)_comp1000362_c0_seq1:3-299(-)
QSLPFPPNYISLSHAGTLSVNPCTAYRLLKDFVSLSTGDFIIQNGANSGVGRVVIQLCKA
WGFKSINIVRDRENLRELVEELSQLGADYTFTPAELRKS

Desire output:

Quote:

comp100001_c0_seq1
comp1000362_c0_seq1

I thought I'd start with a sed command to remove the part of the header line preceding the string "comp", then go on to remove the suffix of the target string (e.g. ":3-509(-)"), followed by an awk command to retain only lines beginning with "comp". But my sed command doesn't do anything and I'm not sure why, so I'm stuck.

Code:

sed -e 's/\>.+_comp/_comp/'

pathunkathunk

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ppmtopgm

ppmtopgm(1)                                                   General Commands Manual                                                  ppmtopgm(1)

NAME

       ppmtopgm - convert a portable pixmap into a portable graymap

SYNOPSIS

       ppmtopgm [ppmfile]

DESCRIPTION

       Reads  a  portable  pixmap  as  input.  Produces a portable graymap as output.  The output is a "black and white" rendering of the original
       image, as in a black and white photograph.  The quantization formula used is .299 r + .587 g + .114 b.

       Note that although there is a pgmtoppm program, it is not necessary for simple conversions from pgm to ppm , because any  ppm  program  can
       read  pgm  (and  pbm  ) files automatically.  pgmtoppm is for colorizing a pgm file.  Also, see ppmtorgb3 for a different way of converting
       color to gray.  And ppmdist generates a grayscale image from a color image, but in a way that makes it easy to differentiate  the  original
       colors, not necessarily a way that looks like a black and white photograph.

QUOTE

       Cold-hearted orb that rules the night
       Removes the colors from our sight
       Red is gray, and yellow white
       But we decide which is right
       And which is a quantization error.

SEE ALSO

       pgmtoppm(1),ppmtorgb3(1),rgb3toppm(1),ppmdist(1),ppm(5),pgm(5)

AUTHOR

       Copyright (C) 1989 by Jef Poskanzer.

                                                                   10 April 2000                                                       ppmtopgm(1)