fu grep

fu-grep

This program's APIs are not finalized.

Usage

  Usage:
  fu-grep [options] Pattern InputFile.fa [...]

  -a, --annotate
     Add comments to the sequence when match is found

  -n, --name 
     Search pattern in sequence name (default: sequence)

  -c, --comments
     Search pattern in sequence comments (default: sequence)

  -s, --stranded
     Do not search reverse complemented oligo

  -f, --fasta
     Force output in FASTA format

  example:
  fu-grep DNASTRING test.fa test2.fa > matched.fa

Examples

• Search for a DNA pattern:

./bin/fu-grep CCA data/compressed.fasta.gz

Output:

>SEQ1_BamHI-EcoRI
acagcgtacgtgatcgacgtagctagctgacgagctagctacacacgatcgtagctggtacacgt

• Search for a DNA pattern and annotate the pattern positions:

./bin/fu-grep -a CCA data/compressed.fasta.gz 

Output:

>SEQ1_BamHI-EcoRI		#matches=1;for=CCA:0;rev=TGG:1
acagcgtacgtgatcgacgtagctagctgacgagctagctacacacgatcgtagctggtacacgt

• Search in the sequence name:

fu-grep -n bam data/compressed.fasta.gz

>SEQ1_BamHI-EcoRI	
acagcgtacgtgatcgacgtagctagctgacgagctagctacacacgatcgtagctggtacacgt

• Search in the sequence "comments":

fu-grep -c len data/comments.fasta

>SEQ1_BamHI-EcoRI	len=65
acagcgtacgtgatcgacgtagctagctgacgagctagctacacacgatcgtagctggtacacgt
>Seq2	len=32
acacacacacacacacacacacacacacacac
>Seq3	len=21
ccccccccccccccccccccc