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Difference between revisions of "Degap.seqs"

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(Revisions)
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==Revisions==
 
==Revisions==
 
* 1.36.0 Adds processors option
 
* 1.36.0 Adds processors option
 +
* 1.40.0 Rewrite of threaded code. Default processors=Autodetect number of available processors and use all available.
  
 
[[Category:Commands]]
 
[[Category:Commands]]

Revision as of 15:30, 29 March 2018

The degap.seqs command reads a fasta file and outputs a .ng.fasta containing the sequences after all gap characters are removed.


Default settings

The fasta parameter is required. You may enter multiple fasta files by separating the names by dashes. Example: fasta=abrecovery.align-amazon.align


mothur > degap.seqs(fasta=abrecovery.align)


If you open abrecovery.ng.fasta you would see:

>AY457915
AGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCATTTAAGACAGATT
ACTTCGGTTTGAAGTCTTTTATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTCATACAGGGGGATA
GCAGCTGGAAACGGCTGGTAATACCGCATAAGCGCACAGTACCACATGGTACAGTGTGAAAAACTCCGGTGGTATGAGA
TGGACCCGCGTCTGATTAGCTTGTTGGCGGGGTAACGGCCCACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGTGAC
CGGCCACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGAGGAAACTC
TGATGCAGCGACGCCGCGTGAGTGAAGAAGTAGTTCGCTATGTAAAGCTCTATCAGCAGGGAAGATAGAGACGGTACCT
GACTAAGAAGCTCCGGCAAATC
>AY457914
TTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCATTTAGAACAGATTACTTC
GGTTTGAAGTTCTTTATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTTGTACTGGGGGATAGCAGC
TGGAAACGGCTGGTAATACCGCATAAGCGCACAATGTTGCATGACATGGTGTGAAAAACTCCGGTGGTATAAGATGGAC
CCGCGTCTGATTAGCTAGTTGGTGAGATAACAGCCCACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGTGACCGGCC
ACATTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGAGGAAACTCTGATG
CAGCGACGCCGCGTGAGTGAAGAAGTAATTCGTTATGTAAAGCTCTATCAGCAGGGAAGATAGAGACGGTACCTAACTA
AGAAGCTCCGGCTAA
>AY457913
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCACTTTTACA
GATTTCTTCGGAATGAAGTTTTAGTGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGTAACCTGCCTCACACAGGGGG
ATAACAGTTGGAAACGGCTGCTAATACCGCATAAGCGCACAGTACCGCATGGTACAGTGTGAAAAACTCCGGTGGTGTG
AGATGGACCCGCGTCTGATTAGCTAGTTGGCAGGGTAACGGCCTACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGT
GACCGGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAA
CCCTGATGCAGCGACGCCGCGTGAGCGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAGAAATGACGG
TACCTGACTAAGAAGCACCGGCAAATCTG
...

processors

The processors option enables you to accelerate the degapping process by using multiple processors. You are able to use as many processors as your computer has with the following option:

mothur > degap.seqs(fasta=abrecovery.align, processors=4)

Revisions

  • 1.36.0 Adds processors option
  • 1.40.0 Rewrite of threaded code. Default processors=Autodetect number of available processors and use all available.