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Degap.seqs

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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. Default processors=Autodetect number of available processors and use all available. You can set processors to 4 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.