Here is a awk command that does the job:

awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} {if ($2) print ">"$0}' input.fas > output.fas

With RS, we declare that the records are separated by >. If the record contains a second line $2 (i.e. is not an empty fasta record), print the record (add a > in front).

edit: just added a missing space for readability. Note that it is also possible to drop the if:

awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} $2 {print ">"$0}' input.fas > output.fas

Perl option:

#!/usr/bin/perl

use strict;
use warnings;

$/="\n>";
while (<>) {
    s/>//g;
    my ($id, $seq) = split (/\n/, $_);
    print ">$_" if (length $seq);
}

run as:

perl filterSeq.pl < FASTA > OUTPUT

You can do it with a simple BioPython script:

#!/usr/bin/env python
from Bio import *
for current_seq in SeqIO.parse("mysequences.fasta", "fasta"):
    if current_seq.seq.tostring() != '':
        print ">", current_seq.id, "\n", current_seq.seq.tostring()

If you have trouble installing Biopython, you can write a plain python script:

#!/usr/bin/env python
current_seq = ''
current_header = ''
for line in open("mysequences.fasta", "r"):
    if line.startswith(">"):
        if current_seq != '':
            print current_header, current_seq,
        current_header = line
        current_seq = ''
    else:
        current_seq += line
if current_seq != '':
    print current_header, current_seq

To run these scripts, just copy and paste them to a file, and then run them from the command line. For example, if you save the second code as "remove_empty_sequences.py", you can execute it by typing:

python remove_empty_sequences.py > outputfile

Note that the script assumes that your input sequences are stored in a file called mysequences.fasta. I'll leave you as an exercise the task of generalizing it for other file names.

PHP code to read sequences from a file (in.txt) and write the output to a file (out.txt)

<?php
$fr = fopen("in.txt", "r");
$text = fread($fr, filesize("in.txt"));
$fw = fopen("out.txt", "w");
while (preg_match("/>[^\n>]{1,}\n>/",$text) === 1)
    {
    $text2 = preg_replace("/>[^\n>]{1,}\n>/",">",$text);
    $text = $text2;
    }
fwrite($fw, $text);
fclose($fr);
fclose($fw);
?>

Hope this helps you too....

Thank you for responding to my question I would want an output in FASTA FORMAT which would contain header followed by a sequence not just the lines of headers alone. I mean a header and then a sequence and so on. I mean the first header should be deleted.The headers from LANL 15 TO 64 must be deleted. I have many similar files like these.

The output should be the following kind. Please let me know if you have understood?

>Throat_LANL_14_orf00002 begin=45 end=212 rf=-3 score=4.34
CTTTACGTAGCGGAAAATTAGATACGGACAGATAAATGTTAGAAGAATTAAATATCGATC
TATCTAGCTTAAAAGCAAATAAAGTAGATAACAGAATATTAGGGGTTGTTNNTTTGACGA
>Throat_LANL_74_orf00002 begin=139 end=264 rf=1 score=0.26
TTTTAAGCTAGATAGATCGATATTTAATTCTTCTAACATTTATCTGTCCGTATCTAATTT
TCCGCTACGTAAAGCGTCAAGTAATGCGTCGCCATCTCCGCTATCCTCACCCTCTTCATC
AGCGTC
>Throat_LANL_80_orf00001 begin=275 end=379 rf=-2 score=2.69
ATATTGATGTCGAAAACAATGATTTCGATATTCCGGTTCATAACCCAGATACGACAGATA
TTGAAGCTGAACTAGGATT

My original file is this

>Throat_LANL_12_orf00001 begin=81 end=9 rf=-3 score=2.57
>Throat_LANL_14_orf00002 begin=45 end=212 rf=-3 score=4.34
CTTTACGTAGCGGAAAATTAGATACGGACAGATAAATGTTAGAAGAATTAAATATCGATC
TATCTAGCTTAAAAGCAAATAAAGTAGATAACAGAATATTAGGGGTTGTTNNTTTGACGA
TCTCCGCTCAAAAGAAAAAGAAGAGATCATTCAATGTGTTTACAATGT
>Throat_LANL_15_orf00001 begin=407 end=125 rf=-2 score=6.05
>Throat_LANL_19_orf00001 begin=394 end=7 rf=2 score=1.93
>Throat_LANL_20_orf00001 begin=651 end=445 rf=2 score=2.78
>Throat_LANL_20_orf00003 begin=455 end=393 rf=-2 score=2.95
>Throat_LANL_37_orf00001 begin=116 end=41 rf=-2 score=1.40
>Throat_LANL_47_orf00001 begin=328 end=139 rf=2 score=0.63
>Throat_LANL_52_orf00001 begin=514 end=148 rf=-1 score=0.31
>Throat_LANL_58_orf00001 begin=208 end=40 rf=2 score=0.56
>Throat_LANL_59_orf00001 begin=316 end=262 rf=2 score=5.28
>Throat_LANL_59_orf00003 begin=338 end=266 rf=-2 score=4.74
>Throat_LANL_64_orf00001 begin=619 end=602 rf=-1 score=2.92
>Throat_LANL_73_orf00002 begin=91 end=222 rf=1 score=0.18
GATCGTCAAANNAACAACCCCTAATATTCTGTTATCTACTTTATTTGCTTTTAAGCTAGA
TAGATCGATATTTAATTCTTCTAACATTTATCTGTCCGTATCTAATTTTCCGCTACGTAA
AGCGTCAAGTAA
>Throat_LANL_74_orf00002 begin=139 end=264 rf=1 score=0.26
TTTTAAGCTAGATAGATCGATATTTAATTCTTCTAACATTTATCTGTCCGTATCTAATTT
TCCGCTACGTAAAGCGTCAAGTAATGCGTCGCCATCTCCGCTATCCTCACCCTCTTCATC
AGCGTC
>Throat_LANL_80_orf00001 begin=275 end=379 rf=-2 score=2.69
ATATTGATGTCGAAAACAATGATTTCGATATTCCGGTTCATAACCCAGATACGACAGATA
TTGAAGCTGAACTAGGATT
>Throat_LANL_82_orf00001 begin=207 end=70 rf=2 score=1.70
>Throat_LANL_83_orf00001 begin=61 end=11 rf=3 score=1.65
>Throat_LANL_88_orf00001 begin=90 end=353 rf=-3 score=0.41
ATATTGATGTCGAAAACAATGATTTCGATATTCCGGTTCATAACCCAGATACGACAGATA
TTGAAGCTGAACTAGGATTAACACGTAGCGACGCTGATGAAGAGGGTGAGGATAGCGGAG
ATGGCGACGCATTACTTGACGCTTTACGTAGCGGAAAATTAGATACGGACAGATAAATGT
TAGAAGAATTAAATATCGATCTATCTAGCTTAAAAGCAAATAAAGTAGATAACAGAATAT
TAGGGGTTGTTNNTTTGACGATCT
>Throat_LANL_96_orf00001 begin=573 end=571 rf=-3 score=2.63
>Throat_LANL_105_orf00001 begin=409 end=128 rf=-1 score=1.85
>Throat_LANL_113_orf00001 begin=69 end=233 rf=3 score=0.86
TCTTCTTTTTCTTTTGAGCGGAGATCGTCAAANNAACAACCCCTAATATTCTGTTATCTA
CTTTATTTGCTTTTAAGCTAGATAGATCGATATTTAATTCTTCTAACATTTATCTGTCCG
TATCTAATTTTCCGCTACGTAAAGCGTCAAGTAATGCGTCGCCAT
>Throat_LANL_121_orf00002 begin=142 end=49 rf=-1 score=3.77
>Throat_LANL_123_orf00002 begin=85 end=30 rf=-1 score=2.77
>Throat_LANL_126_orf00001 begin=120 end=314 rf=3 score=8.14
TGTTATCTACCTCTTCATCAGCGTCGCTACGTGTTAATCCTAGTTCAGCTTCAATATCTG
TCGTATCTGGGTTAT

Thank you in advance

>Throat_LANL_133_orf00002 begin=309 end=258 rf=-3 score=1.12
>Throat_LANL_135_orf00001 begin=182 end=295 rf=-2 score=0.40
TATTGAAGCTGAACTAGGATTAACACGTAGCGACGCTGATGAAGAGGGTGAGGATAGCGG
AGATGGCGACGCATTACTTGACGCTTTACGTAGCGGAAAATTAGATACGGACAG