sort.seqs

The sort.seqs command puts sequences from a fasta, name, count, group, quality, flow or taxonomy file in the same order.

Options

The command will generate a *.sorted.* file. You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads.

accnos option

To use the accnos option, follow this example:

mothur > sort.seqs(accnos=order.accnos, fasta=GQY1XT001.shhh.trim.fasta)

count option

The count file is used to represent the number of duplicate sequences for a given representative sequence.

mothur > sort.seqs(fasta=GQY1XT001.shhh.trim.unique.align, count=GQY1XT001.shhh.trim.count_table)

fasta option

To use the fasta option, follow this example:

mothur > sort.seqs(accnos=order.accnos, fasta=GQY1XT001.shhh.trim.fasta)

flow option

To use the flow option, follow this example:

mothur > sort.seqs(accnos=order.accnos, fasta=GQY1XT001.shhh.trim.fasta, flow=GQY1XT001.shhh.trim.flow)

taxonomy option

To use the taxonomy option, follow this example:

mothur > sort.seqs(accnos=order.accnos, fasta=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.pick.fasta, taxonomy=GQY1XT001.shhh.trim.unique.good.filter.unique.precluster.pick.rdp.taxonomy)

qfile option

To use the qfile option, follow this example:

mothur > sort.seqs(accnos=order.accnos, fasta=GQY1XT001.shhh.trim.fasta, qfile=GQY1XT001.shhh.trim.qual)

large

The large parameter indicates your files are too large to fit in RAM, default=F.

mothur > sort.seqs(accnos=order.accnos, fasta=GQY1XT001.shhh.trim.fasta, qfile=GQY1XT001.shhh.trim.qual, large=T)

name - not recommended

The name option allows you to provide a name file.

We DO NOT recommend using the name file. Instead we recommend using a count file. The count file reduces the time and resources needed to process commands. It is a smaller file and can contain group information.

group - not recommended

The group parameter allows you to provide a group file.

We DO NOT recommend using the name / group file combination. Instead we recommend using a count file. The count file reduces the time and resources needed to process commands. It is a smaller file and can contain group information.

Revisions

  • 1.24.0 - First introduced.
  • 1.28.0 - Added count option
  • 1.40.0 - Allow for () characters in taxonomy definitions. #350
  • 1.47.0 - Fixes crash with sort.seqs if multiple seqs present with the same name.