fastAQ

fastAQ is a fast and super lightweight package for working with FASTA/FASTQ sequences.

Download :

    git clone https://github.com/Jverma/fastAQ
or  https://pypi.python.org/pypi/fastaq

Install :

         python setup.py develop 
    or   pip install fastaq

Dependencies : None

Documentation : https://pythonhosted.org/fastaq/

Command line Usage:

git clone https://github.com/Jverma/fastAQ

Notation/Variables:

location = location of the fastAQ folder on your computer.
fasta = location/fastAQ/fastAQ/commandLineTools/fasta.py
fastq = location/fastAQ/fastAQ/commandLineTools/fasta.py
fastq2fasta = location/fastAQ/fastAQ/commandLineTools/fastq2fasta.py

Conver a FASTQ file into a FASTA file

python $fastq2fasta input_file.fastq 

List containing the names/headers of all the sequences in the FASTA/Q file.

python $fasta input_file.fasta -seqNames 
python $fastq input_file.fastq -seqNames

Sequences corresponding to the names/headers in a text file.

python $fasta input_file.fasta -seq names_file.txt
python $fastq input_file.fastq -seq names_file.txt

Qualities of the sequences corresponding to the names/headers in a text file.

python $fastq input_file.fastq -qual names_file.txt

Trim sequences corresponding to the names in a text file according to the intervals in another file.

python $fasta input_file.fasta -trim names_file.txt interval_file.txt
python $fastq input_file.fastq -trim names_file.txt interval_file.txt

Mask sequences corresponding to the names in a text file according to the intervals in another file.

python $fasta input_file.fasta -mask names_file.txt interval_file.txt
python $fastq input_file.fastq -mask names_file.txt interval_file.txt

Reverse Complement sequences corresponding to the names in a text file.

python $fasta input_file.fasta -reverseComplement names_file.txt
python $fastq input_file.fastq -reverseComplement names_file.txt

Reverse Complement all the sequences in the given file.

python $fasta input_file.fasta -reverseComplementAll
python $fastq input_file.fastq -reverseComplementAll

Trim all the sequences in the given file (remove intervalStart bases from left and intervalEnd bases from right).

python $fasta input_file.fasta -trimAll -intervalStart=1 -intervalEnd=5
python $fastq input_file.fastq -trimAll -intervalStart=1 -intervalEnd=5

Mask all the sequences in the given file (masks intervalStart bases from left and intervalEnd bases from right).

python $fasta input_file.fasta -maskAll -intervalStart=1 -intervalEnd=5
python $fastq input_file.fastq -maskAll -intervalStart=1 -intervalEnd=5

Trim FASTQ sequences in the file by removing low quality bases (quality > qualityCutOff).

python $fastq input_file.fastq -trimLowQuality names_file.txt -qualityCutOff=30

Trim FASTQ sequences according to the Mott's algorithm (choose limitValue)

python $fastq input_file.fastq -mottTrim names_file.txt -limitValue=0.65

Trim all FASTQ sequences by removing low quality bases.

python $fastq input_file.fastq -trimAlllowQuality -qualityCutOff=30

Trim all FASTQ sequences by Mott's algorithm.

python $fastq input_file.fastq -mottTrimAll -limitValue=0.65