count_fasta
usage: bash count_fasta.sh FASTA
DESCRIPTION: Script counts number of sequences in a FASTA file
DEPENDENCIES:
count_fasta has no dependencies
EXAMPLES:
bash ~/stanford_swc/count_fasta.sh ~/stanford_swc/fasta-o-matic/fasta/normal.fa
N50
usage: N50.py FASTA
DESCRIPTION: Script calculates N50 for a FASTA file.
DEPENDENCIES:
fasta_o_matic.py runs with either python2.7+ or python3.3+
EXAMPLE:
Calculate N50 :
python ~/stanford_swc/N50.py ~/stanford_swc/fasta-o-matic/fasta/normal.fa
Fasta-O-Matic
Cite as: Jennifer M Shelton (2015). FASTA tools including Fasta-O-Matic
usage: fasta_o_matic.py [-h] [-v] [-q] [-c] -f FILE [-s STEPS [STEPS ...]][-o OUT_DIR]
DESCRIPTION: Script runs quality checking and filtering based on a user- defined list of quality checks. Command-line options that may be omitted (i.e. are NOT required) are shown in square brackets. The actively maintained version of Fasta-O-Matic is at : https://github.com/i5K-KINBRE-script-share/read-cleaning-format-conversion
DEPENDENCIES:
fasta_o_matic.py runs with either python2.7+ or python3.3+
DETAILS:
optional arguments:
-h, --help show this help message and exit
-v, --verbose Runs reporting status updates
-q, --quiet Does not report status updates
-c, --colorized Colorizes log reports. Use only if printing output to
screen.
-f FILE, --fasta FILE
This is the the full path (path and filename) of the
user provided FASTA file.
-s STEPS [STEPS ...], --qc_steps STEPS [STEPS ...]
List of QC steps to perform on FASTA file (default= -s
wrap new_line header_whitespace).
-o OUT_DIR, --out_dir OUT_DIR
Output directory for any repaired FASTA created (no
trailing slash).
EXAMPLES:
Make output directory (your re-formatted FASTA files will be created here) :
mkdir ~/out_stanford_swc
Fix FASTA file with inconsistantly wrapped sequence lines and remove spaces in headers:
python3 ~/stanford_swc/fasta-o-matic/fasta_o_matic.py -f ~/stanford_swc/fasta-o-matic/fasta/miswrapped.fa -c -o ~/out_stanford_swc -s wrap header_whitespace
Fix FASTA file with missing end of line character for last sequence:
python2.7 ~/stanford_swc/fasta-o-matic/fasta_o_matic.py -f ~/stanford_swc/fasta-o-matic/fasta/missing_last_new_line.fa -c -o ~/out_stanford_swc -s new_line
Fix unwrapped FASTA file:
python ~/stanford_swc/fasta-o-matic/fasta_o_matic.py -f ~/stanford_swc/fasta-o-matic/fasta/unwrapped.fa -c -o ~/out_stanford_swc -s wrap new_line header_whitespace
Remove spaces in FASTA headers:
python ~/stanford_swc/fasta-o-matic/fasta_o_matic.py -f ~/stanford_swc/fasta-o-matic/fasta/missing_last_new_line.fa -c -o ~/out_stanford_swc -s header_whitespace