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fastascripts – Manipulate FASTA files

These scripts were never meant to see the light of day. I apologize for the distasteful code.

Utilities

  • facanon Output the lexicographically smaller of the sequence and its reverse complement
  • facat Concatenate FASTA files and add a prefix to the identifier
  • fachain Merge overlapping sequences
  • faclean Reformat and optionally remove short contigs from a FASTA file
  • facmp Compare pairs of sequences
  • facstont Convert colour-space sequence to nucleotides
  • fadecimate Randomly keep 1 in every N pairs of reads
  • faget Select sequences from a FASTA file by identifier
  • fagrep Search a FASTA file using a regular expression
  • fakmer Generate tiled k-mers
  • falength Print the lengths of sequences
  • falint Check the syntax of a FASTA file
  • famd5 Calculate a MD5 digest for a FASTA file
  • famd5seq Calculate a MD5 digest for each sequence
  • fanttocs Convert nucleotides to colour-space sequence
  • farand Generate a FASTA file with random sequence
  • farc Reverse and complement the sequences
  • farenumber Renumber the sequences
  • faseperate-mates Separate paired reads into two files
  • fasplit-read Split a read into two at the midpoint
  • fastqtofa Convert a FASTQ file to FASTA format
  • fatoagp Convert FASTA scaffolds to FASTA contigs and an AGP file
  • fatofastq Convert a FASTA file to a FASTQ file
  • fatoseq Remove FASTA headers
  • faunamb Convert IUPAC-IUB ambiguity codes to ACGT
  • faunscaffold Break scaffolds into contigs at Ns

License

Copyright 2013 Shaun Jackman

Permission to use, copy, modify, and/or distribute this software for any purpose with or without fee is hereby granted, provided that the above copyright notice and this permission notice appear in all copies.