Perl Script To Remove Unnecessary Headers

A FASTA file containing:

>ppa020722m pacid=19 locus=ppa020722m.g ID=ppa020722m.v1.0 annot-version=v1.0
CTCCAACAAGCCTTCACCAACATCCAAAATCATTGCTCTGGTTTCCTGCACCACCTCTCTCACTTTCCTGTCTTCAACCC
CAACCCCTCTTCCCTCAAAACCCAACTCGAGTCCACCTTCGCCAACCTCCAAAACCAAG
>ppa020723m pacid=10 locus=ppa020723m.g ID=ppa020723m.v1.0 annot-version=v1.0
CTCCAACAAGCCTTCACCAACATCCAAAATCATTGCTCTGGTTTCCTGCACCACCTCTCTCACTTTCCTGTCTTCAACCC
CAACCCCTCTTCCCTCAAAACCCAACTCGAGTCCACCTTCGCCAACCTCCAAAACCAAG
>ppa020724m pacid=15 locus=ppa020724m.g ID=ppa020724m.v1.0 annot-version=v1.0
CTCCAACAAGCCTTCACCAACATCCAAAATCATTGCTCTGGTTTCCTGCACCACCTCTCTCACTTTCCTGTCTTCAACCC
CAACCCCTCTTCCCTCAAAACCCAACTCGAGTCCACCTTCGCCAACCTCCAAAACCAAG
......

Can anybody provide a Perl script to clean the headers in this FASTA database to make an output file as:

>ppa020722m
CTCCAACAAGCCTTCACCAACATCCAAAATCATTGCTCTGGTTTCCTGCACCACCTCTCTCACTTTCCTGTCTTCAACCC
CAACCCCTCTTCCCTCAAAACCCAACTCGAGTCCACCTTCGCCAACCTCCAAAACCAAG
>ppa020723m
CTCCAACAAGCCTTCACCAACATCCAAAATCATTGCTCTGGTTTCCTGCACCACCTCTCTCACTTTCCTGTCTTCAACCC
CAACCCCTCTTCCCTCAAAACCCAACTCGAGTCCACCTTCGCCAACCTCCAAAACCAAG
>ppa020724m
CTCCAACAAGCCTTCACCAACATCCAAAATCATTGCTCTGGTTTCCTGCACCACCTCTCTCACTTTCCTGTCTTCAACCC
CAACCCCTCTTCCCTCAAAACCCAACTCGAGTCCACCTTCGCCAACCTCCAAAACCAAG
......

Many thanks.

perl fasta

• 4,906 views • link

updated 4.7 years ago by Ram

• written 12.3 years ago by redspider19800915 •

what have you tried?

• 24 views • link

written 12.3 years ago by Michael Dondrup

Forget perl, just use cut.

• 0 views • link

written 12.3 years ago by Devon Ryan

3 answers

perl -ane 'print "$F[0]\n";' yourFile.fa > yourFile.clean.fa

• 106 views • link

written 12.3 years ago by David Langenberger

as dpryan79 suggested, you can use cut -d " " -f 1 input.fasta

• 14 views • link

written 12.3 years ago by Prakki Rama

There you go:

• 77 views • link

updated 4.7 years ago by Ram

• written 12.3 years ago by umer.zeeshan.ijaz

Also awk alternative:

awk '/>/{$0=$1}1' test.fasta

• 63 views • link

updated 4.7 years ago by Ram

• written 12.3 years ago by umer.zeeshan.ijaz

Or if there are no line breaks in the sequences:

awk '{print $1}' file.fasta > output.fasta

• 0 views • link

updated 4.7 years ago by Ram

• written 12.3 years ago by 5heikki

More posts like this

VEP custom annotation - synonymous file
written 4.1 years ago by Sowmya Pulapet •

Hello everyone, I am using Ensembl-Vep tool with custom annotation feature for variant annotation. However, I got several warnings instead of the output WARNING: Chromosome …
Getting warning during tblastn
written 11.2 years ago by seta

Dear all, I'm trying to do tblastn (ncbi-blast2-2-30+ version) using fasta sequences of protein as a query and my de novo assembled transcriptome as a …
Problem With Counting Mapped Reads
written 12.4 years ago by njs531 •

Hi, This is my very first experience analysing RNAseq data. My goal is to do differential analysis between two strains of a bacteria. So far, …
Biopython: Change Sequence Id And Print Out New Sequence
written 12.4 years ago by QVINTVS_FABIVS_MAXIMVS

I'm learning biopython and I'm having trouble with reassigning the seq_record.id variable for my sequence. <pre><code>from Bio import SeqIO for seq_record in SeqIO.parse(file, "fasta"): seq_record.id …
How To Fix A Tophat "Glist Error That Is Likely Caused By Incorrect Sequence Naming
written 13.2 years ago by Jirapong •

I'm trying to map sample against Xenopus Laevis from Xenbase.org (latest version 6.0). They provided GFF3 and FASTA file. which look like following FASTA <pre><code>> …
Difficult To Download Gene Sequences From Ncbi
written 13.3 years ago by jcastrofigueroa

Hello everyone: I'm having a problem trying to download gene sequences from the Gene database at NCBI website using biopyhon. I iniciated the code by …
Samlocusiterator Skips Every Second Locus
written 13.5 years ago by Johan

I'm writing some Scala code which uses the SamLocusIterator after a excellent tip here: <a href='/p/64310/#64316'>A: Java fasta reference iterator</a> However I'm getting some pretty …
Go Term Enrichment Analysis For Ath1121501
written 13.7 years ago by suganyasivagurunathan •

Iam trying to do a enrichment analysis and working with data from ath1121501 (arabidopsis) arrays.I have problems in defining the universe and the selected genes …
Tophat / Cufflinks Not Using Gene_Id Or Gene_Name From Gtf File
written 13.7 years ago by Owen S.

I am trying to get tophat / cufflinks to work with Ensembl annotations. Although this looks like a long post, my problem is quite …
Extracting Fasta Sequence Using Biopython
written 14.7 years ago by Ma

Hi: I want to extract one section of a chromosome into a FASTA file, I have two versions, but neither of them work correctly. At …