We will be offering mothur and R workshops throughout 2019. Learn more.

Degap.seqs

From mothur
Revision as of 19:59, 15 July 2015 by Westcott (Talk | contribs)

Jump to: navigation, search

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