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Top Forums UNIX for Beginners Questions & Answers How to count the length of fasta sequences? Post 303033626 by RavinderSingh13 on Tuesday 9th of April 2019 09:24:20 AM
Old 04-09-2019
Quote:
Originally Posted by dineshkumarsrk
Thank you singh,
Your command prints all the sequences. However, I need to print only few sequences length as listed in id.txt file. If I did not understand your commands properly, please let me know, where to include id.txt file in your command?
Oh ok, I was in impression that you want to print all seq strings length in a single Input_file, could you please try following now.
Code:
awk 'FNR==NR{a[$0];next} /^>/ && sub(/^>/,""){;found=val="";if($0 in a){val=$0;found=1};next} found{print val,length($0)} ' ids.txt  Input_file

Output will be as follows.
Code:
seq1 6
seq2 7

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
 

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NIFTI_STATS(1)							   User Commands						    NIFTI_STATS(1)

NAME
nifti_stats - compute NIfTI statistical functions SYNOPSIS
nifti_stats [-q|-d|-1|-z] value CODE [p1 p2 p3] DESCRIPTION
nifti_stats supports several distributions (normal, uniform, logistic, chi, etc.) and calculates density or cummulative distribution func- tion (and many more). Values are printed to stdout and can be piped to other tools. value can be a single number or in the form bot:top:step. default ==> output p = Prob(statistic < val). -q ==> output is 1-p. -d ==> output is density. -1 ==> output is x such that Prob(statistic < x) = val. -z ==> output is z such that Normal cdf(z) = p(val). -h ==> output is z such that 1/2-Normal cdf(z) = p(val). Allowable CODEs: CORREL, TTEST, FTEST, ZSCORE, CHISQ, BETA, BINOM, GAMMA, POISSON, NORMAL, FTEST_NONC, CHISQ_NONC, LOGISTIC, LAPLACE, UNIFORM, TTEST_NONC, WEIBULL, CHI, INVGAUSS, EXTVAL, PVAL, LOGPVAL and LOG10PVAL Following CODE are distributional parameters, as needed. Results are written to stdout, 1 number per output line. EXAMPLE
Piping output into AFNI program 1dplot: nifti_stats -d 0:4:.001 INVGAUSS 1 3 | 1dplot -dx 0.001 -stdin SEE ALSO
libnifti(1), nifti_tool(1), nifti1_test(1). Homepage: http://niftilib.sourceforge.net AUTHOR
RW Cox - SSCC/NIMH/NIH/DHHS/USA/EARTH - March 2004 This manual page was written by Michael Hanke <michael.hanke@gmail.com>, for the Debian project (but may be used by others). nifti_stats September 2007 NIFTI_STATS(1)
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