FastXScripts

Scripts that I needed to change Fasta/FastQ files during my PhD

Usage

filter_fastx.py

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_fastx.py

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)

complement.py

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)

wtf.py

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)