FASTX-toolkit
http://hannonlab.cshl.edu/fastx_toolkit/
	-used mainly to manipulate sequence reads from illumina sequencers
	-most of the tools can handle fasta and fastq files

	-commandline
		-on perun
			-conda environment
				-source activate fastx_toolkit
					fastx_clipper -h
	-online graphical interface
http://hannonlab.cshl.edu/fastx_toolkit/galaxy.html
https://usegalaxy.org/

	-local downloads
http://hannonlab.cshl.edu/fastx_toolkit/download.html
	




DOES NOT WORK WITH LOWERCASE nucleotides


DOES NOT WORK with interleaved sequences

DOES NOT WORK WITH AMINO ACIDS

-common syntax
	-i for input file
	-o for output file
	-h for help 

fastx_clipper
[-l N]       = discard sequences shorter than N nucleotides. default is 5

more p2.fasta 
\\ 
  >sequence1 blahblah
  ACGTACGTACGTACGTACGTACGTT
  >sequence47 bluhbluhbluh
  TTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCC
  >myfavourite
  AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
  >myfav2
  AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
  >contig23 acanth
  AGTAGTGACTGAGTAATAGACGTAG	

fastx_clipper -i p2.fasta -o blah -l 50

more blah
  >sequence47 bluhbluhbluh
  TTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCC

fastx_renamer
	-renames the sequences
		-n TYPE
			-default or SEQ uses sequence as name
			-COUNT uses counter
	-the extra information on the header line is lost

more p2.fasta 
  >sequence1 blahblah
  ACGTACGTACGTACGTACGTACGTT
  >sequence47 bluhbluhbluh
  TTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCC
  >myfavourite
  AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
  >contig23 acanth
  AGTAGTGACTGAGTAATAGACGTAG

fastx_renamer -i p2.fasta -o p2renamed.fasta -n SEQ
  >ACGTACGTACGTACGTACGTACGTT
  ACGTACGTACGTACGTACGTACGTT
  >TTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCC
  TTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCC
  >AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
  AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
  >AGTAGTGACTGAGTAATAGACGTAG
  AGTAGTGACTGAGTAATAGACGTAG

fastx_renamer -i p2.fasta -o p2renamed.fasta -n COUNT
  >1
  ACGTACGTACGTACGTACGTACGTT
  >2
  TTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCCCC
  >3
  AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG
  >4
  AGTAGTGACTGAGTAATAGACGTAG



fasta_formatter
	-can change multiline sequences (interleaved) to single line sequences (sequential)
	-can change the length of interleaved lines

more p5.fasta 
  >M86863.1
  GTAACATGACGTTGACCGTGCGGGGCTACATGTAGCAGCTGGGTGTGCTAACTACGGATACATGCCTACA
  ACCCCCACAAGTCAAGACCATTGCGACGCGGAAACAGGAGCCCGCAAAAGAGGAGAAAAACAACGGCGAG 
  >seq2
  ACTCGGGGGCGGAGTGGGTCACGTGACTTTCCTTTTTCCCCTCACCTGGCCCGCTCCGTCCATATCTCTG
  TCGTACAAGACAATATTGTCGCAACGCAAAAGGTCCATAAATTACTGGGTAGACGCAACTCTATTTGAAG
  GCAACCTACCGTTTGCTTTTAGTGTTTTGGTTTTGTTACCATATCCAAAAAAAAACCATATATCCAAAAA
  TTCCGCTGCACCATCTCTTCTTCTCTCCATCAACTACCCCTGCGGAGAAATTCACACCACAGTTACAATG


fasta_formatter -i p5.fasta -o p5oneline
  >M86863.1
  GTAACATGACGTTGACCGTGCGGGGCTACATGTAGCAGCTGGGTGTGCTAACTACGGATACATGCCTACAACCCCCACAAGTCAAGACCATTGCGACGCGGAGGG
  >seq2
  ACTCGGGGGCGGAGTGGGTCACGTGACTTTCCTTTTTCCCCTCACCTGGCCCGCTCCGTCCATATCTCTGTCGTACAAGACAATATTGTCGCAACGCAAAAGGTC

fasta_formatter -i p5.fasta -o p5.20 -w 20
  >M86863.1
  GTAACATGACGTTGACCGTG
  CGGGGCTACATGTAGCAGCT
  GGGTGTGCTAACTACGGATA
  CATGCCTACAACCCCCACAA
  GTCAAGACCATTGCGACGCG
  GAAACAGGAGCCCGCAAAAG
  AGGAGAAAAACAACGGCGAG
  >seq2
  ACTCGGGGGCGGAGTGGGTC
  ACGTGACTTTCCTTTTTCCC
  CTCACCTGGCCCGCTCCGTC
  CATATCTCTGTCGTACAAGA
  CAATATTGTCGCAACGCAAA
  AGGTCCATAAATTACTGGGT
  AGACGCAACTCTATTTGAAG
  GCAACCTACCGTTTGCTTTT
  AGTGTTTTGGTTTTGTTACC
  ATATCCAAAAAAAAACCATA
  TATCCAAAAATTCCGCTGCA
  CCATCTCTTCTTCTCTCCAT
  CAACTACCCCTGCGGAGAAA
  TTCACACCACAGTTACAATG



fastx_trimmer
	-first and last base to keep
		-default is entire read
		-f first base to keep
			-1=first base
		-l last base to keep
			-based on the entire read before -f

more p6.fasta 
  >seq1
  AAAAAAAAAATTTTTTTTTTGGGGGGGGGG
  >seq2
  CCCAAATTTGGGCCCAAATTTGGG

fastx_trimmer -i p6.fasta -o p6.trimmed -f 10
  >seq1
  ATTTTTTTTTTGGGGGGGGGG
  >seq2
  GGGCCCAAATTTGGG

fastx_trimmer -i p6.fasta -o p6.trimmed -f 10 -l 15
  >seq1
  ATTTTT
  >seq2
  GGGCCC




fastx_reverse_complement
	-reverse complements the sequences
		-does both
more p7.fasta 
  >seq1
  AAAAAAAAAAGGGGGGGGGG
  >seq2
  AGAGAGTT


fastx_reverse_complement -i p7.fasta -o p7rc
  >seq1
  CCCCCCCCCCTTTTTTTTTT
  >seq2
  AACTCTCT