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.