get.seqs

The get.seqs command takes a list of sequence names (.accnos file) and either a fastq, fasta, name, group, list, count or align.report file to generate a new file that contains only the sequences in the list. This command may be used in conjunction with the list.seqs command to help screen a sequence collection. To complete this analysis, you need to download the folder compressed in the Esophagus.zip archive.

Options

To run get.seqs, you must provide the accnos option and at least one other option. The command will generate a *.pick.* file. To generate an accnos file, let’s first run unique.seqs, summary.seqs, screen.seqs, and list.seqs:

mothur > unique.seqs(fasta=esophagus.fasta)

mothur > summary.seqs(fasta=esophagus.unique.fasta)

       Start   End NBases  Ambigs  Polymer
Minimum:   1   831 831 0   4
2.5%-tile: 1   841 841 0   4
25%-tile:  1   857 857 0   5
Median:    1   866 866 0   5
75%-tile:  1   870 870 0   5
97.5%-tile:    1   900 900 5   7
Maximum:   1   1378    1378    20  8
# of Seqs: 656

mothur > screen.seqs(fasta=esophagus.unique.fasta, maxambig=0)

mothur > list.seqs(fasta=esophagus.unique.good.fasta)

This generates esophagus.unique.good.accnos, a file with 527 sequences.

A .accnos file is simply a list of file names that meets some given criterion (see list.seqs for further detail). If you have a subset of sequences that are of interest to you, and you want to retrieve them sequences from a larger .fasta file, another option for generating a .accnos file is to create your list (a single column of names) in a text editor or spreadsheet program that allows you to save your work as tab-delimited text. Notepad and Excel both allow you to do this, just be sure to use quotation marks around your file name in order to get your .accnos file type designation (e.g. “My_subset_sequences.accnos”).

accnos option

To use the accnos option, follow this example:

mothur > get.seqs(accnos=esophagus.unique.good.accnos, fasta=esophagus.fasta)

This generates the file esophagus.pick.fasta, which contains the following lines:

>9_1_12
GCAAGTCGAGGGGAAAC...
>9_1_14
GCAAGTCGAGGGGAACG...
>9_1_15
GCAAGTCGAGGGGAAAC...
...

fasta option

To use the fasta option, follow this example:

mothur > get.seqs(accnos=esophagus.unique.good.accnos, fasta=esophagus.fasta)

This generates the file esophagus.pick.fasta, which contains the sequences from esophagus.unique.good.accnos.

name option

To use the name option, follow this example:

mothur > get.seqs(accnos=esophagus.unique.good.accnos, name=esophagus.names)

This generates the file esophagus.pick.names, which contains the following lines:

65_5_22    65_5_22
65_5_12    65_5_12
59_7_23    59_7_23
59_7_7 59_7_7
65_5_28    65_5_28
65_9_13    65_9_13
9_6_11 9_6_11
...

dups

The dups parameter is only be used in tandem with a namefile. By default dups is true, so if any sequence in a specific line in the name file is in your .accnos file, then all sequences in that line will be kept. This is especially useful when used with the groupfile, since for most commands your files can contain only the unique sequences, but the groupfile need to contain all the sequences in your namefile. For example, let’s look at the following line from the esophagus.unique.good.accnos:

65_1_2 65_1_2,65_1_23,65_2_1,65_2_8

if dups is set to false, only 65_1_2 will be added to your files, but if dups is true, then 65_1_2,65_1_23,65_2_1,65_2_8 will all be added.

count option

The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence. It can also contain group information.

mothur > get.seqs(accnos=esophagus.unique.good.accnos, count=esophagus.count_table)

group option

To use the group option, follow this example:

mothur > get.seqs(accnos=esophagus.unique.good.accnos, group=esophagus.groups)

This generates the file esophagus.pick.groups, which contains the following lines:

9_1_12 B
9_1_14 B
9_1_15 B
9_1_16 B
9_1_18 B
...

alignreport option

To use the alignreport option, follow this example:

mothur > get.seqs(accnos=esophagus.unique.good.accnos, alignreport=esophagus.align.report)

This generates the file esophagus.pick.align.report, which contains the following lines:

QueryName  QueryLength TemplateName    TemplateLength  SearchMethod    SearchScore AlignmentMethod QueryStart  QueryEnd    TemplateStart   TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate  LongestInsert   SimBtwnQuery&Template   
9_1_12 866 108139  1525    kmer    62.17   needleman   1   866 50  917 868 2   0   0   91.36   
9_1_14 847 134265  1524    kmer    65.71   needleman   1   847 50  896 849 2   2   0   90.81   
9_1_15 866 108139  1525    kmer    61.47   needleman   1   866 50  917 869 3   1   1   91.02   
9_1_16 854 13820   1555    kmer    90.67   needleman   1   854 43  897 859 5   4   1   97.56   
...

list option

To use the list option, follow this example:

mothur > get.seqs(accnos=esophagus.unique.good.accnos, list=esophagus.fn.list)

This generates the file esophagus.fn.pick.list, which contains the following lines:

unique 480 9_6_14,9_1_12   9_1_14  9_1_15  9_1_16  9_1_18  9_1_19  9_1_20  9_1_26  9_1_27  ... 
0.00   265 9_4_14,9_7_28,9_1_26,9_6_14,9_1_12  9_2_20,9_1_14   9_1_15  9_1_16 ...
0.01   115 9_1_15,9_6_25,9_3_24,9_4_14,9_7_28,9_1_26,9_6_14,9_1_12 65_7_10,65_1_30,9_6_15,9_8_20, ...
...

taxonomy option

To use the taxonomy option, follow this example:

mothur > get.seqs(accnos=esophagus.unique.good.accnos, taxonomy=esophagus.silva.full.taxonomy)

This generates the file esophagus.silva.full.pick.taxonomy, which contains the following lines:

9_1_12 Bacteria(100);Bacteroidetes-Chlorobi(100);Bacteroidetes(100);Bacteroides-Prevotella(100);...
9_1_14 Bacteria(100);Bacteroidetes-Chlorobi(100);Bacteroidetes(100);Bacteroides-Prevotella(100);...
9_1_15 Bacteria(100);Bacteroidetes-Chlorobi(100);Bacteroidetes(100);Bacteroides-Prevotella(100);...
9_1_16 Bacteria(100);Firmicutes(100);Clostridia(100);Acidaminococcaceae(100);Veillonella(100);...

qfile option

The qfile option allows you to select sequences from your quality file, and can be used as follows:

mothur > get.seqs(accnos=esophagus.unique.good.accnos, qfile=esophagus.qual)

fastq option

The fastq option allows you to select sequences from your fastq file.

contigsreport

The contigsreport option allows you to select sequences from your contigsreport file.

Revisions

  • 1.28.0 Added count option
  • 1.30.0 Bug Fix: dups=f could cause sequence name mismatches between new fasta and name files.
  • 1.31.1 Bug Fix: dups=f, renaming issue, https://forum.mothur.org/viewtopic.php?f=3&t=2371
  • 1.33.0 Added fastq option
  • 1.37.0 Checks for repeat sequences names and eliminates them. Allows users creating their own templates to easily remove duplicate sequences from their reference files. #159
  • 1.40.0 - Allow for () characters in taxonomy definitions. #350
  • 1.44.0 - Adds contigsreport option. #660