How To Grep A Specific Contig From A List?

Question

[Bdv]

Hi

I have a list of contigs and want to extract one contig (by its title). What is the exact command for that?

Thanks!

[Giovanni M Dall'Olio]

if your contig file is in fasta format, there are a lot of discussion already open. Have a search in the archives.

Answer 1

[User 59]

This has already been addressed as Giovanni pointed out:

• Perl solution
• Python solution
• Fasta parsing in Perl
• Extracting multiple entries from a fasta file

Please try at least a cursory search of the site before posting a new question!

Answer 2

[Alex]

Default grep can't find multiline patterns.

You can use pcregrep.

Check this topic from stackoverflow.

Answer 3

[Giulio Genovese]

If you want to extract multiple contigs at different times, it is highly suggested that you build an index. Here some commands:

samtools faidx in.fasta #(create an index for the fasta file with all the contigs)
samtools faidx in.fasta contigname > contigname.fasta #(extract the single contig you need)

Answer 4

[Vashar]

#to extract seqnames from MS blast result(seqtool) files:
grep contigname filename > out.txt

If you need more lines from contig add -A number after grep like: (for 3 lines)

grep -A 3 contigname filename > out.txt

[Michael Schubert]

This is impractical. A better solution would be to use a regex like >CONTIG_NAME[^>]+ but only if the engine supports multi-line matching (i.e., not the Unix grep tool).

[Ketil]

I've used agrep for this (as in: agrep -d '^>' pattern contigs.fasta) but unfortunately it is unreliable, and has some ugly limitations. I also implemented my own tool (sgrep, part of the biohaskell stuff)