Removing duplicate sequences and modifying a text file Post: 302964554

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Top Forums Shell Programming and Scripting Removing duplicate sequences and modifying a text file Post 302964554 by RavinderSingh13 on Friday 15th of January 2016 12:33:17 PM

01-15-2016

Moderator

Hello 4galaxy7,

Could you please try following and let me know if this helps you.

Code:

awk '/^>TCONS/{gsub(/TCONS_.*gene/,"gene",$0);split($0, A,"_");A[2]=++i;printf("%s %06d\n", A[1], A[2]);next} 1'  Input_file

Output will be as follows.

Code:

>gene=XLOC 000001
AATTGTGGTGAAATGACTTCTGTTAACGGAGACATCGATGATTGTTGTTACTATTTGTTCTCAGGATTCA
TTTGTCCGGTTCATACCCCGGACGGCGCCCCTTGCGGGCTGCTCAATCACCTGACAATGAACTGTATCGT
CACGAAGCATCCGGATCGCAAATTAAAGGCTGCGCTACCAACGGTGCTGGTGGATCTAGGAATGCTTCCG
TTGTCTGTTGCGAATAATTGGAAGGACTCGTACACGGTAATGCTGAATGGTAAAGTGATCGGCCTGATCG
AAGATAATATTGTTGATAAGGTGGCCCGCAAACTAAGGCAGCTGAAGATAATTGGTGAAGAGGTGCCGAA
CACGTTGGAGATCGCGCTGGTGCCGAAGAGGAAGG
>gene=XLOC 000002
CGGATGTATATCGTGCCGTGCTTTGATCGTTTATTTGATGTCCCATTTGCTGTTGGACTTGCGGCGGTAT
TGCCGTTGTTCTCGGCCTTGGTCGTGGCCGTGTGTCTTGCGTGTTTAGGTCCGGGCTGTCTTGAGCACCA
ACTTCCAGTGTCGGTAGTGGAGCTCGTGGTTGCAGGGTTTGCTGCCGAGTTCGTTGGGGCGTTTTGATTG
TTAGGCCTCGTGAACTCGTTTTTTTCGACGCAGATATTGATTTCGAAGGTGTGTGTCTCCTTTCCTGCGG
TTGTTTCGTTTGTTTTGTCGTCGACGGCTCGACGTATTTCGTTGTACTTGAGGTGTCTTTGTTTTGTCGA
TCTTTGTTTCGATCGAGTATATTCCCAACGTTGTGGACGTTGGTCTTCATTCTTCTTATTTCAAATATTA
TATTTTTCCGGCGTTCCTCAAGATATTGGAGGCACCGTTGTTCTCTTTCGCGAAGTCGCGTGAACTCTTC
>gene=XLOC 000003
TGGGTGAAGGTGCTGTGAGCCGTAAAACTTGTAAAAAGTGGTTTCAGAAGTTTCGGAATGGCGATTTCGA
TCTTACTGATCGCGAACGCAGTGGAATGCCGAGAAAAGTTGAAGACGAGGAACTGGAGCAACTATTGAAC
GAGAATCCTTGTAAGACGCAACAAGAACTTGCTGAGCAACTTGGTGTAACTCAACAAGCTATTTCCGTTC
GCTTAAAAAAGCTTGGAAGAATTTCCAAGGCAGGCCGTTGGGTTCCTCATGTGTTCAGCCCCAAACACAA
AGCGAGACGCTGTGACATTAGAATAACTAACCATGGTCAGTCAGTTTGCTTACGGCTTATGTCTTAAAGC
AAGGTTGTAAACAAGAACTTATCTCTTGTCTATGATCTTGCTTTAAAATATAAATAGTAATTAAATTGAC
CAACTACGATCGTTTATTGGAAGAATAATCGATCGTGGTTGGTTAGGTTATGTTTCACAATACGTCGTAT
GTCGCTGTCGG

Thanks,
R. Singh

RavinderSingh13

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LEARN ABOUT DEBIAN

ppmquantall

ppmquantall(1)						      General Commands Manual						    ppmquantall(1)

NAME

       ppmquantall - run ppmquant on a bunch of files all at once, so they share a common colormap

SYNOPSIS

       ppmquantall [-ext extension] ncolors ppmfile ...

DESCRIPTION

       Takes a bunch of portable pixmap as input.  Chooses ncolors colors to best represent all of the images, maps the existing colors to the new
       ones, and overwrites the input files with the new quantized versions.

       If you don't want to overwrite your input files, use the -ext option.  The output files are then named the same as the input files, plus  a
       period and the extension text you specify.

       Verbose	explanation:  Let's  say  you've got a dozen pixmaps that you want to display on the screen all at the same time.  Your screen can
       only display 256 different colors, but the pixmaps have a total of a thousand or so different colors.  For a single pixmap you  solve  this
       problem	with  ppmquant;  this  script  solves  it for multiple pixmaps.  All it does is concatenate them together into one big pixmap, run
       ppmquant on that, and then split it up into little pixmaps again.

       (Note that another way to solve this problem is to pre-select a set of colors and then use ppmquant's -map option  to  separately  quantize
       each pixmap to that set.)

SEE ALSO

       ppmquant(1), ppm(5)

AUTHOR

       Copyright (C) 1991 by Jef Poskanzer.

								   27 July 1990 						    ppmquantall(1)