Hi, I have this problem. I have a fasta file containing the whole genome of a arabidopsis plant. I also have a list of genes I need to extract the sequences from the fasta file. Each line contains 2 or 3 or 4 sequences. I need to create a fasta file for each of the sequences in the each line. Any help? I visualize it for simplicity.
sequences I need to get fast for:
AT1G63760 AT1G05890 AT2G31510
AT3G30122 AT1G08410 AT2G27200
AT1G56390 AT1G09210
AT1G18191
AT3G32445 AT1G18500 AT1G74040
AT2G34760 AT1G20010 AT1G75780 AT1G74040
AT1G60480 AT1G23490 AT1G70490
AT4G10414 AT1G33230 AT4G10430
AT4G06748 AT1G52410 AT3G15950
AT2G06822 AT1G52930 AT3G15460
AT3G43820 AT1G62810 AT4G12290
AT2G11280 AT1G63640 AT5G41310
AT2G15120 AT2G15090 AT4G34250
>AT1G63760
ATGATGGATTCCGATGATGATATGCTCGATGCCCACGATATGGACTCGGTAGATTATGATTTTGACAGCGGCGGCACCGATGATGACAAC
>AT1G05890
GCAAAAGTCCATATATCTTTCTCTCATCTACTCGATTTCTGAATCGCGAACGCAGCGAGC
GATCCGGAATCGAGAGAGAGAGCTACCAATTTTTCCAACTTGTTCGGTTCCTTATAAAGC
TGTTTACTTTCCCTTGCGAATTCTCTCTCTCTCTACTATAAAGCAATACCCTTTTCTTTC
TTTTTTGGTAACCCCCAAACCCTACTTTGTCCAGCGAGAAAGGAAGAGGGGTTTCGTCTG
>AT2G31510
ATGGATTCTGAAGAAGACATGCTCGATGCGCACGATATGGAGTCTGGAGAGGATGATTTC
TACAGCGGTGGAACTGATGATTGTAATGATAGTGATGATGGTGAACCTGATTATGGGTTT
GTTGAGGAAGATGCTGATGATTCTGCTATGATCGCCTCTCATCGCTCTCAGGTGGGTTTT
TGTTTTTGTTTCTTAATTCATTTTGGTGTTGGTTGTTGAAGCTAATTGCTTTTAGAACTC
>AT1G18191
AAAATTGAAGACGAAGAGTTTAAGACTCTATCAGATCAGAAGGTCTCTATTTTCTCGAAACGTCGGCTTTAGAGAACCAAAACGTC
>AT1G56390
GCAATGGTGAAACTAGACTCTAAACTCATCTCTATGATTGTTTTCGGTATCGTGGTAATCGTCTCTGCTG
>AT1G09210
GCTAGCTCCTCTCCTCGCGGTATATATAAGCTCCAGGTCTTGTACATCTTCATCATCTGA
TCTCGGGGAAGCTCCGATCTGAGTTTTTTTTAGCAATGGCGAAAATGATTCCTAGCCTCG
TCTCTCTAATTCTTATCGGTCTTGTTGCGATCGCCTCCGCCGCAGTTATTTTCGAGGAGC
GCTTTGATGGTATCTAATTTCTACATCTCTATCTCTATACTCTATCTTCCTGATGATGCG
>AT2G34760
ATGCGTAAACAAAGTTTTAAGATAGTTATGATTCGTTTTTTGAGAGTCAATAACAAAAATTATCCGATC
>AT1G20010
AACAGAGACAATTGGTTATATTAGCTGTCACTCCCATCTTTCATATTCCTTCACCATCTC
TCTCTCTCTCGATCTTGTGAACCACTACACACACTAACACAATGAGAGAGATCCTTCACA
TTCAAGGTGGTCAATGCGGTAACCAGATTGGTTCCAAGTTCTGGGAAGTCATCTGCGACG
AGCACGGCATCGATTCCACCGGACGTTACAGTGGAGACACTGCAGATCTCCAGCTTGAAC
GTATCAATGTCTATTACAATGAAGCTTCAGGTGGAAGATACGTTCCTCGTGCTGTTCT
>AT1G75780
ATCTCCAGATCCCAAAATCTTCATCGATCATCATCATCATGAGAGAAATCCTCCACGTCC
AAGGCGGCCAATGCGGTAACCAAATCGGTTCCAAATTCTGGGAAGTTATCTGCGACGAAC
ACGGCGTTGATCCCACCGGACGTTACAACGGTGATTCCGCCGATCTTCAGCTCGAACGTA
TCAATGTTTATTACAATGAAGCTTCTGGTGGTCGTTACGTTCCTCGTGCTGTTCTCATGG
>AT1G74040
AAAGTAGTAACCAGAGACACTGTGCCGTCGCCCGTCGCCGCCGCCGCCACACTATCATCT
CTCTCAGGTTTTTGATTTTCCACGGCAATGGAGTCTTCGATTCTCAAAAGCCCTAATCTC
TCTTCACCATCGTTCGGTGTACCTTCAATTCCCGCCTTATCCTCCTCCTCCACCTCACCA
TTTTCATCTCTTCATCTCCGATCACAGAACCACCGTACCATCTCTCTTACCACCGCCGGA
AAATTCCGTGTCTCGTATTCTCTCTCCGCTTCTTCACCTCTACCACCTCATGCTCCTCGC
CGTCGTCCCAATTACATCCCTAACCGTATATCCGATCCCAATTACGTCAGAATCTT
If I understand the question correctly, you want to create a separate fasta file for each line in your list of IDs and the file will contain the number of sequences listed on the line.
You have 2 choices when trying to match an ID list to a fasta file of sequences.
The first approach becomes very slow for many sequences, since you have to loop through all sequences for each ID. So it's generally better to index the sequence file.
Install Bioperl and index the fasta file, seqs.fa, using this command:
bp_index -dir . seqs.idx seqs.fa
Now you can open the file of IDs, ids.txt, split each line on space and use bp_fetch to pull each ID in turn from the index and write to a new fasta file. Something like this should work:
#!/usr/bin/perl -w
use strict;
open INFILE, "ids.txt";
while(<INFILE>) {
chomp;
my @ids = split(/\s+/);
my $outfile = join("_", @ids).".fa";
open OUTFILE, ">$outfile";
foreach my $id(@ids) {
print OUTFILE `bp_fetch -dir . seqs.idx:$id`;
}
close OUTFILE;
}
close INFILE
In this example, each new fasta file will be named according to the IDs on each line, separated by underscores; e.g. AT1G56390_AT1G09210.fa.
Hi I tried your script and this is the error I get. Can't exec "bp_fetch": No such file or directory at script_test.pl line 16, [?] line 1. print() on closed filehandle OUTFILE at script_test.pl line 16, [?] line 1. I can not understand why as I am not so familiar with bioperl. Thanks again for your help
notseq from EMBOSS can read in a multi sequence file and a list of identifiers (wildcards) and write the non matching sequences to one file the matching ones to a different file (-junkout). You want the junkout file. You can specify a file with the identifiers to filter e.g. '@names.dat'.
this is the command that you need:
ruby -nae 'system("notseq -sequence fasta.txt -sformat1 fasta -osformat fasta -osname ignore.fasta -junkoutseq "+ $..to_s()+".matches.fasta -auto -exclude "+$F.join(",")) ' identifiers.txt
If you use Bioperl and SeqIO you can have your fasta file stored as a proper data structure (alternatively you can write your own fasta parser and store the sequences in a hash of your own).
Parsing the IDs is simple, process each line, on each line split on whitespace so you have an array of IDs. Then it is a simple matter of grabbing the sequences from the hash using the ID key and printing them to a file.
I prefer keeping my sequences in a hash data structure myself over Bio::SeqIO in most cases as I can easily pull out sequences by their ID given a list of IDs.
di you try the Sequence Bulk Download and Analysis for Arabidopsis ?
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What have you tried so far? Have you looked at the related questions on the right?
Hi have script pick up a sequence per line. Not sure how to modify it so that I can have many sequences per line picked up and then saved in many files each file for 1 line of sequences.
!/usr/bin/perl -w
use strict;
my $idsfile = "gene1.txt"; my $seqfile = "TAIR9seq.fasta"; my %ids = ();
open (OUT,">selectionseqs.fasta");
open FILE, $idsfile; while([?]) { chomp; $ids{$_} += 1; } close FILE;
local $/ = "n>";
open FASTA, $seqfile; while ([?]) { chomp; my $seq = $_; my ($id) = $seq =~ /^>(S+)/; if (exists($ids{$id})) { $seq =~ s/^>.+n//; $seq =~ s/n//g; print "$seqn"; print "$seqn"; print OUT ">$idn$seqn"; } } close FASTA;