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
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