faSomeRecords

Extracts FASTA records from multiFASTA file based on a list of FASTA headers

Inspired by the C++ version of faSomeRecords from kentUtils

Python version:

Download just the program

wget https://raw.githubusercontent.com/santiagosnchez/faSomeRecords/master/faSomeRecords.py

Download the whole repo and install

git clone https://github.com/santiagosnchez/faSomeRecords.git
cd faSomeRecords
sudo ln -s `pwd`/faSomeRecords.py /usr/local/bin/faSomeRecords

Help message

    python faSomeRecords.py -h
    usage: faSomeRecords.py [-h] --fasta FASTA_FILE [--list LIST] [--records [RECORD ...]] [--outfile [OUTFILE]] [--stdout]
                            [--keep-list-order] [--exclude]

    Retrieves some FASTA records provided a FASTA file and a list or records.

    optional arguments:
      -h, --help            show this help message and exit
      --fasta FASTA_FILE, -f FASTA_FILE
                            FASTA file where all the sequences are stored.
      --list LIST, -l LIST  file name of the list.
      --records [RECORD ...], -r [RECORD ...]
                            individual FASTA records.
      --outfile [OUTFILE], -o [OUTFILE]
                            name for output file (default: records.fasta)
      --stdout, -s          if sequences should be printed to screen.
      --keep-list-order     will keep the list order. The default is to keep the fasta order. (defaut:False)
      --exclude, -e         exclude sequences in the list.

    Records can be sepcified providing a list file with --list/-l
    or one by one in the command line using --records/-r.

    All sequences are now kept in the same input order. So the --keep flag no longer applies

    The elements in the list must be an exact match as those in the
    master FASTA file, and may or may not include the ">" character at
    the begining of the header.

    Example of list file:
    sequence1
    sequence2
    sequence3
    ...
    sequenceN

Examples

# print 3 sequences to screen
./faSomeRecords.py -f examples/example_20_seqs.fa -r seq_1 seq_3 seq_5 --stdout
# keep list input order
./faSomeRecords.py -f examples/example_20_seqs.fa -r seq_10 seq_4 seq_15 --stdout --keep-list-order
# take sequences from a list to default output file
./faSomeRecords.py -f examples/example_20_seqs.fa -l examples/get_these.txt
# exclude sequences in list, print the rest to screen
./faSomeRecords.py -f examples/example_1000_seqs.fa -l examples/exclude_these.txt --stdout
# test a bigger file
./faSomeRecords.py -f examples/example_30000_seqs.fa -r seq_1 seq_3 seq_5 --stdout

In the list file you must have only the headers without the > character. For example:

seq_1
seq_2
seq_3
seq_4
...
seq_1000

Although you can leave the > character and faSomeRecords will remove it for you.

Pretty straight forward.

Perl version

No longer maintained

I recommend using the Python version! Which is the one that will be developed and supported further on.

Download

wget https://raw.githubusercontent.com/santiagosnchez/faSomeRecords/master/faSomeRecords.pl

Help message

perl faSomeRecords.pl -h

Try:
perl faSomeRecords.pl -f multiFASTA   FASTA file with sequences
	                  -l list         A list of headers that match -f
        	          -o outfile      Name your output file