Scripts that I needed to change Fasta/FastQ files during my PhD
Filter Fasta/FastQ file for IDs or length of read
usage: filter_fastx.py [-h] (-i IDS | -l LENGTH | -s LENGTH) [-o FASTX] FASTX
Filter FASTA or FASTQ file for ids or length of reads
positional arguments:
FASTX Multi FASTQ or FASTA file
optional arguments:
-h, --help show this help message and exit
-i IDS, --read_ids IDS
One read ID per line in file, line separated read IDs (default: None)
-l LENGTH, --long LENGTH
Filter FASTA or FASTQ file for reads given length or longer (default: None)
-s LENGTH, --short LENGTH
Filter FASTA or FASTQ file for reads given length or shorter (default: None)
-o FASTX, --outFASTX FASTX
FASTQ or FASTA file containing provided reads (default: None)
Slice subsequences by their position from reads in Fasta/FastQ.
usage: slice_fastx.py [-h] [--append] [--lowerbound LOWERBOUND] [--upperbound UPPERBOUND] [--position POSITION] [--range RANGE] [--id ID] inFastx outFastx
positional arguments:
inFastx Fastx file from which to slice subsequences
outFastx Fastx file to write slices
options:
-h, --help show this help message and exit
--append Appends slices to existing outFastx (default: False)
--lowerbound LOWERBOUND
Lower bound for slicing area (1-based) (default: None)
--upperbound UPPERBOUND
Upper bound for slicing area (1-based) (default: None)
--position POSITION Position which to slice (1-based) (default: None)
--range RANGE Range which to slice up- and downstream from the position (default: None)
--id ID Fastx ID filter to slice from specific sequence (only works for one ID) (default: None)
Translate nucleotide sequences from terminal or fasta files.
usage: complement.py [-h] [--reverse] sequences
positional arguments:
sequences Input sequence separated with "," or fasta file
optional arguments:
-h, --help show this help message and exit
--reverse Use to print 3'->5' sequence. (default: False)
--rna Translate RNA sequences (default: False)
What the fasta will analyse given sequences for their content like number of bases, the AT and GC content, the number of ambiguous bases (e.g. N).
What the fasta will analyse your reference fasta sequence
positional arguments:
FASTA_or_SEQ FASTA reference file or sequence
options:
-h, --help show this help message and exit
--rna switch to RNA if reference FASTA contains RNA (default: False)