I wrote a simple script, fastaRegexFinder.py, to look for regular expressions in a fasta file, the format you have should be ready to go. However, it looks for one regex pattern at a time. You could run one motif at a time, serially or in parallel, or chain several motifs together, like 'AC[TA]G|CC[TA]G|ACG'. (I should edit it to take multiple regexes...)
This is from the script's help:
fastaRegexFinder.py -h
usage: fastaRegexFinder.py [-h] --fasta FASTA [--regex REGEX] [--matchcase]
[--noreverse] [--maxstr MAXSTR]
[--seqnames SEQNAMES [SEQNAMES ...]] [--quiet]
[--version]
DESCRIPTION
Search a fasta file for matches to a regex and return a bed file with the
coordinates of the match and the matched sequence itself.
By default, fastaRegexFinder.py searches for putative G-quadruplexes on forward
and reverse strand using the quadruplex rule described at
http://en.wikipedia.org/wiki/G-quadruplex#Quadruplex_prediction_techniques.
The default regex is '([gG]{3,}\w{1,7}){3,}[gG]{3,}' and along with its
complement they produce the same output as in
http://www.quadruplex.org/?view=quadbaseDownload
Output bed file has columns:
1. Name of fasta sequence (e.g. chromosome)
2. Start of the match
3. End of the match
4. ID of the match
5. Length of the match
6. Strand
7. Matched sequence as it appears on the forward strand
For matches on the reverse strand it is reported the start and end position on the
forward strand and the matched string on the forward strand (so the G4 'GGGAGGGT'
present on the reverse strand is reported as ACCCTCCC).
Note: Fasta sequences (chroms) are read in memory one at a time along with the
matches for that chromosome.
The order of the output is: chroms as they are found in the inut fasta, matches
sorted within chroms by positions.
EXAMPLE:
## Test data:
echo '>mychr' > /tmp/mychr.fa
echo 'ACTGnACTGnACTGnTGAC' >> /tmp/mychr.fa
fastaRegexFinder.py -f /tmp/mychr.fa -r 'ACTG'
mychr 0 4 mychr_0_4_for 4 + ACTG
mychr 5 9 mychr_5_9_for 4 + ACTG
mychr 10 14 mychr_10_14_for 4 + ACTG
fastaRegexFinder.py -f /tmp/mychr.fa -r 'ACTG' --maxstr 3
mychr 0 4 mychr_0_4_for 4 + ACT[3,4]
mychr 5 9 mychr_5_9_for 4 + ACT[3,4]
mychr 10 14 mychr_10_14_for 4 + ACT[3,4]
less /tmp/mychr.fa | fastaRegexFinder.py -f - -r 'A\w\wGn'
mychr 0 5 mychr_0_5_for 5 + ACTGn
mychr 5 10 mychr_5_10_for 5 + ACTGn
mychr 10 15 mychr_10_15_for 5 + ACTGn
DOWNLOAD
fastaRegexFinder.py is hosted at http://code.google.com/p/bioinformatics-misc/
optional arguments:
-h, --help show this help message and exit
--fasta FASTA, -f FASTA
Input fasta file to search. Use '-' to read the file from stdin.
--regex REGEX, -r REGEX
Regex to be searched in the fasta input.
Matches to the reverse complement will have - strand.
The default regex is '([gG]{3,}\w{1,7}){3,}[gG]{3,}' which searches
for G-quadruplexes.
--matchcase, -m Match case while searching for matches. Default is
to ignore case (I.e. 'ACTG' will match 'actg').
--noreverse Do not search the reverse complement of the input fasta.
Use this flag to search protein sequences.
--maxstr MAXSTR Maximum length of the match to report in the 7th column of the output.
Default is to report up to 10000nt.
Truncated matches are reported as <ACTG...ACTG>[<maxstr>,<tot length>]
--seqnames SEQNAMES [SEQNAMES ...], -s SEQNAMES [SEQNAMES ...]
List of fasta sequences in --fasta to
search. E.g. use --seqnames chr1 chr2 chrM to search only these crhomosomes.
Default is to search all the sequences in input.
--quiet, -q Do not print progress report (i.e. sequence names as they are scanned).
--version, -v show program's version number and exit
