Sponsored Content
Top Forums UNIX for Beginners Questions & Answers How to count the length of fasta sequences? Post 303033673 by RavinderSingh13 on Wednesday 10th of April 2019 07:23:49 AM
Old 04-10-2019
Hello dineshkumarsrk,

Could you please try following.
Code:
awk '
FNR==NR{
  if($0~/^>/){
    sub(/^>/,"")
    val=$0;
    next
  }
  a[val]=(a[val]?a[val] OFS:"")length($0)
  next
}
($0 in a){
  print $0,a[$0]
}
'  Input_file  id.txt

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

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Extract length wise sequences from fastq file

I have a fastq file from small RNA sequencing with sequence lengths between 15 - 30. I wanted to filter sequence lengths between 21-25 and write to another fastq file. how can i do that? (4 Replies)
Discussion started by: empyrean
4 Replies

2. Shell Programming and Scripting

Shell script for changing the accession number of DNA sequences in a FASTA file

Hi, I am having a file of dna sequences in fasta format which look like this: >admin_1_45 atatagcaga >admin_1_46 atatagcagaatatatat with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
Discussion started by: margarita
5 Replies

3. Shell Programming and Scripting

Extract sequences from a FASTA file based on another file

I have two files. File1 is shown below. >153L:B|PDBID|CHAIN|SEQUENCE RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM DIGTTHDDYANDVVARAQYYKQHGY >16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Discussion started by: nelsonfrans
7 Replies

4. Shell Programming and Scripting

Count and search by sequence in multiple fasta file

Hello, I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table... (5 Replies)
Discussion started by: empyrean
5 Replies

5. Shell Programming and Scripting

Shorten header of protein sequences in fasta file

I have a fasta file as follows >sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3 MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM KGVTSTRVYERA >sp|L18484|AP2A2_RAT AP-2... (3 Replies)
Discussion started by: alexypaul
3 Replies

6. UNIX for Dummies Questions & Answers

Select distinct sequences from fasta file and list

Hi How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this: >H8V34IS02I59VP SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA... (6 Replies)
Discussion started by: Marion MPI
6 Replies

7. Shell Programming and Scripting

Getting unique sequences from multiple fasta file

Hi, I have a fasta file with multiple sequences. How can i get only unique sequences from the file. For example my_file.fasta >seq1 TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC >seq2... (3 Replies)
Discussion started by: Ibk
3 Replies

8. Shell Programming and Scripting

Outputting sequences based on length with sed

I have this file: >ID1 AA >ID2 TTTTTT >ID-3 AAAAAAAAA >ID4 TTTTTTGGAGATCAGTAGCAGATGACAG-GGGGG-TGCACCCC Add I am trying to use this script to output sequences longer than 15 characters: sed -r '/^>/N;{/^.{,15}$/d}' The desire output would be this: >ID4... (8 Replies)
Discussion started by: Xterra
8 Replies

9. Shell Programming and Scripting

Shorten header of protein sequences in fasta file to only organism name

I have a fasta file as follows >sp|Q8WWQ8|STAB2_HUMAN Stabilin-2 OS=Homo sapiens OX=9606 GN=STAB2 PE=1 SV=3 MMLQHLVIFCLGLVVQNFCSPAETTGQARRCDRKSLLTIRTECRSCALNLGVKCPDGYTM ITSGSVGVRDCRYTFEVRTYSLSLPGCRHICRKDYLQPRCCPGRWGPDCIECPGGAGSPC NGRGSCAEGMEGNGTCSCQEGFGGTACETCADDNLFGPSCSSVCNCVHGVCNSGLDGDGT... (3 Replies)
Discussion started by: jerrild
3 Replies

10. UNIX for Beginners Questions & Answers

How to add specific bases at the beginning and ending of all the fasta sequences?

Hi, I have to add 7 bases of specific nucleotide at the beginning and ending of all the fasta sequences of a file. For example, I have a multi fasta file namely test.fasta as given below test.fasta >TalAA18_Xoo_CIAT_NZ_CP033194.1:_2936369-2939570:+1... (1 Reply)
Discussion started by: dineshkumarsrk
1 Replies
Complex(3o)							   OCaml library						       Complex(3o)

NAME
Complex - Complex numbers. Module Module Complex Documentation Module Complex : sig end Complex numbers. This module provides arithmetic operations on complex numbers. Complex numbers are represented by their real and imaginary parts (carte- sian representation). Each part is represented by a double-precision floating-point number (type float ). type t = { re : float ; im : float ; } The type of complex numbers. re is the real part and im the imaginary part. val zero : t The complex number 0 . val one : t The complex number 1 . val i : t The complex number i . val neg : t -> t Unary negation. val conj : t -> t Conjugate: given the complex x + i.y , returns x - i.y . val add : t -> t -> t Addition val sub : t -> t -> t Subtraction val mul : t -> t -> t Multiplication val inv : t -> t Multiplicative inverse ( 1/z ). val div : t -> t -> t Division val sqrt : t -> t Square root. The result x + i.y is such that x > 0 or x = 0 and y >= 0 . This function has a discontinuity along the negative real axis. val norm2 : t -> float Norm squared: given x + i.y , returns x^2 + y^2 . val norm : t -> float Norm: given x + i.y , returns sqrt(x^2 + y^2) . val arg : t -> float Argument. The argument of a complex number is the angle in the complex plane between the positive real axis and a line passing through zero and the number. This angle ranges from -pi to pi . This function has a discontinuity along the negative real axis. val polar : float -> float -> t polar norm arg returns the complex having norm norm and argument arg . val exp : t -> t Exponentiation. exp z returns e to the z power. val log : t -> t Natural logarithm (in base e ). val pow : t -> t -> t Power function. pow z1 z2 returns z1 to the z2 power. OCamldoc 2012-06-26 Complex(3o)
All times are GMT -4. The time now is 07:39 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy