Sponsored Content
Full Discussion: fasta format?
Top Forums UNIX for Dummies Questions & Answers fasta format? Post 302281007 by lost on Wednesday 28th of January 2009 03:35:21 AM
Old 01-28-2009
fasta format?

Hi,
I'm in need of creating a file in the fasta format:
Code:
>1A6A.A      
HVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITN
VPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCR
VEHWGLDEPLLKHWEF
>1A6A.B    
PRFLEYSTSECHFFNGTERVRYLDRYFHNQEENVRFDSDVGEFRAVTELGRPDAEYWNSQKDLLEQKRGRVDNYCRHNYG

Thinking it could be possible using awk... Just don't have it right at all below since it's only printing the first 60 positions in the line and not making the full line into several lines of 60 positions.
Code:
cat filename | awk '{print substr($1,1,60)}'

I also need to add a '>' to the first line with the lineID
Right now my file is in this format:
Code:
DRB1_010101
MVCLKLPGGSCMTALTVTLMVLSSPLALAGDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLLFLGAGLFIYFRNQKGHSGLQPTGFLS

Help! and thanks!
 

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

grep FASTA files

I would like to extract the sequences larger than 10 bases but shorter than 18 along with the identifier from a FASTA file that looks like this: > Seq I ACGACTAGACGATAGACGATAGA > Seq 2 ACGATGACGTAGCAGT > Seq 3 ACGATACGAT I know I can extract the IDs alone with the following code grep... (3 Replies)
Discussion started by: Xterra
3 Replies

2. Shell Programming and Scripting

Changing from FASTA to PHYLIP format

I really need some help with this task. I have a bunch of FASTA files with hundreds of DNA sequences that look like this: >SeqID1 AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC TGACAGGTTCAAAGGCTGCAGTGCAGTGACGTGACGATTT >Sequence 22... (13 Replies)
Discussion started by: Xterra
13 Replies

3. UNIX for Dummies Questions & Answers

renaming (renumbering) fasta files

I have a fasta file that looks like this: >Noname ACCAAAATAATTCATGATATACTCAGATCCATCTGAGGGTTTCACCACTTGTAGAGCTAT CAGAAGAATGTCAATCAACTGTCCGAGAAAAAAGAATCCCAGG >Noname ACTATAAACCCTATTTCTCTTTCTAAAAATTGAAATATTAAAGAAACTAGCACTAGCCTG ACCTTTAGCCAGACTTCTCACTCTTAATGCTGCGGACAAACAGA ... I want to... (2 Replies)
Discussion started by: Oyster
2 Replies

4. UNIX for Dummies Questions & Answers

How to change sequence name in along fasta file?

Hi I have an alignment file (.fasta) with ~80 sequences. They look like this- >JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0 GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
Discussion started by: baika
2 Replies

5. Shell Programming and Scripting

Extract sequence from fasta file

Hi, I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help . input > fefrwefrwef X900 AGAGGGAATTGG AGGGGCCTGGAG GGTTCTCTTC > fefrwefrwef X932 AGAGGGAATTGG AGGAGGTGGAG GGTTCTCTTC > fefrwefrwef X937... (2 Replies)
Discussion started by: ritakadm
2 Replies

6. UNIX for Dummies Questions & Answers

Fasta header modification

Hi, I need some help with modifying fasta headers. I have a fasta file with thousands of contigs and I need to modify their headers with the information obtained from a second file. File 1 contains the fasta sequences: >contig0001 length=11115 numreads=10777 agatgtagatctct... (6 Replies)
Discussion started by: Lokaps
6 Replies

7. UNIX for Dummies Questions & Answers

Round up -FASTA file

I have the following script: awk 'FNR==NR{s+=$3;next;} { print $1 , $2, 100*$3/s }' and the following file: >P39PT-1224 Freq 900 cccctacgacggcattggtaatggctcagctgctccggatcccgcaagccatcttggatatgagggttcgtcggcctcttcagccaagg-cccccagcagaacatccagctgatcg >P39PT-784 Freq 2... (2 Replies)
Discussion started by: Xterra
2 Replies

8. Shell Programming and Scripting

Help with reformat single-line multi-fasta into multi-line multi-fasta

Input File: >Seq1 ASDADAFASFASFADGSDGFSDFSDFSDFSDFSDFSDFSDFSDFSDFSDFSD >Seq2 SDASDAQEQWEQeqAdfaasd >Seq3 ASDSALGHIUDFJANCAGPATHLACJHPAUTYNJKG ...... Desired Output File >Seq1 ASDADAFASF ASFADGSDGF SDFSDFSDFS DFSDFSDFSD FSDFSDFSDF SD >Seq2 (4 Replies)
Discussion started by: patrick87
4 Replies

9. UNIX for Beginners Questions & Answers

How to count the length of fasta sequences?

I could calculate the length of entire fasta sequences by following command, awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta But, I need to calculate the length of a particular fasta sequence specified/listed in another txt file. The results to to be... (14 Replies)
Discussion started by: dineshkumarsrk
14 Replies

10. UNIX for Beginners Questions & Answers

How to append two fasta files?

I have two fasta files as shown below, File:1 >Contig_1:90600-91187 AAGGCCATCAAGGACGTGGATGAGGTCGTCAAGGGCAAGGAACAGGAATTGATGACGGTC >Contig_98:35323-35886 GACGAAGCGCTCGCCAAGGCCGAAGAAGAAGGCCTGGATCTGGTCGAAATCCAGCCGCAG >Contig_24:26615-28387... (11 Replies)
Discussion started by: dineshkumarsrk
11 Replies
IGAWK(1)							 Utility Commands							  IGAWK(1)

NAME
igawk - gawk with include files SYNOPSIS
igawk [ all gawk options ] -f program-file [ -- ] file ... igawk [ all gawk options ] [ -- ] program-text file ... DESCRIPTION
Igawk is a simple shell script that adds the ability to have ``include files'' to gawk(1). AWK programs for igawk are the same as for gawk, except that, in addition, you may have lines like @include getopt.awk in your program to include the file getopt.awk from either the current directory or one of the other directories in the search path. OPTIONS
See gawk(1) for a full description of the AWK language and the options that gawk supports. EXAMPLES
cat << EOF > test.awk @include getopt.awk BEGIN { while (getopt(ARGC, ARGV, "am:q") != -1) ... } EOF igawk -f test.awk SEE ALSO
gawk(1) Effective AWK Programming, Edition 1.0, published by the Free Software Foundation, 1995. AUTHOR
Arnold Robbins (arnold@skeeve.com). Free Software Foundation Nov 3 1999 IGAWK(1)
All times are GMT -4. The time now is 03:52 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy