chop.seqs

The chop.seqs command reads a fasta file and outputs a .chop.fasta containing the trimmed sequences. It works on both aligned and unaligned sequences.

Default settings

The chop.seqs command parameters are fasta, fastq, name, group, count, numbases, countgaps and keep. fasta or fastq is required unless you have a valid current file. numbases is also required.

mothur > chop.seqs(fasta=abrecovery.fasta, numbases=100)

mothur > chop.seqs(fastq=test.fastq, numbases=100)

Options

qfile

The qfile option to allows for chopping quality files associated with your fasta file.

mothur > chop.seqs(fasta=abrecovery.fasta, qfile=abrecovery.qual, numbases=100)

numbases

The numbases parameter is required, and indicates the number of bases you want to keep.

keep

The keep parameter is set to front by default, meaning you want to keep the front of the sequence. You can also set keep to back.

Here’s what abrecovery.fasta looks like before the chop.seqs command:

>AY457915
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGC
ATTTAAGACAGATTACTTCGGTTTGAAGTCTTTTATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGT
AACCTGCCTCATACAGGGGGATAGCAGCTGGAAACGGCTGGTAATACCGCATAAGCGCACAGTACCACAT
GGTACAGTGTGAAAAACTCCGGTGGTATGAGATGGACCCGCGTCTGATTAGCTTGTTGGCGGGGTAACGG
CCCACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCA
GACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGAGGAAACTCTGATGCAGCGACGCCGCGTG
AGTGAAGAAGTAGTTCGCTATGTAAAGCTCTATCAGCAGGGAAGATAGAGACGGTACCTGACTAAGAAGC
TCCGGCAAATC

>AY457914
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGC
ATTTAGAACAGATTACTTCGGTTTGAAGTTCTTTATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGT
AACCTGCCTTGTACTGGGGGATAGCAGCTGGAAACGGCTGGTAATACCGCATAAGCGCACAATGTTGCAT
GACATGGTGTGAAAAACTCCGGTGGTATAAGATGGACCCGCGTCTGATTAGCTAGTTGGTGAGATAACAG
CCCACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCA
GACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGAGGAAACTCTGATGCAGCGACGCCGCGTG
AGTGAAGAAGTAATTCGTTATGTAAAGCTCTATCAGCAGGGAAGATAGAGACGGTACCTAACTAAGAAGC
TCCGGCTAA

>AY457913
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGC
ACTTTTACAGATTTCTTCGGAATGAAGTTTTAGTGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGTAA
CCTGCCTCACACAGGGGGATAACAGTTGGAAACGGCTGCTAATACCGCATAAGCGCACAGTACCGCATGG
TACAGTGTGAAAAACTCCGGTGGTGTGAGATGGACCCGCGTCTGATTAGCTAGTTGGCAGGGTAACGGCC
TACCAAGGCGACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCAAA
CTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGGGAAACCCTGATGCAGCGACGCCGCGTGAG
CGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAGAAATGACGGTACCTGACTAAGAAGC
ACCGGCAAATCTG

>AY457912
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGC
ATTTGCGACAGATTTCTTCGGATTGAAGTTGCTTATGACTGAGTGGCGGACGGGTGAGTAACGCGTGGGT
AACCTGCCTCACACAGGGGGATAGCAGTTGGAAACGGCTGATAATACCGCATAAGCGCACAGTACCGCAT
GGTACAGTGTGAAAAACTCCGGTGGTGTGAGATGGACCCGCGTCTGATTAGCTTGTTGGCAGGGTAACGG
CCTACCAAGGCAACGATCAGTAGCCGACCTGAGAGGGTGACCGGCCACATTGGGACTGAGACACGGCCCA
GACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGAGGAAACTCTGATGCAGCGACGCCGCGTG
AGTGAAGAAGTAATTCGTTATGTAAAGCTCTATCAGCAGGGAAGATAGTGACGGTACCTGACTAAGAAGC
TCCGGCTAATCGT

Here’s what abrecovery.chop.fasta looks like after running:

 mothur > chop.seqs(fasta=abrecovery.fasta, numbases=100, keep=front)

>AY457915
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCATTTAAGACAGATTACTTCGGTTTGAAGT
>AY457914
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCATTTAGAACAGATTACTTCGGTTTGAAGT
>AY457913
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCACTTTTACAGATTTCTTCGGAATGAAGTT
>AY457912
CCCTTAGAGTTTGATCCTGGCTCAGGATGAACGCTGGCGGCGTGCTTAACACATGCAAGTCGAACGAAGCATTTGCGACAGATTTCTTCGGATTGAAGT

Here’s what abrecovery.chop.fasta looks like after running:

 mothur > chop.seqs(fasta=abrecovery.fasta, numbases=100, keep=back)

>AY457915
ATGCAGCGACGCCGCGTGAGTGAAGAAGTAGTTCGCTATGTAAAGCTCTATCAGCAGGGAAGATAGAGACGGTACCTGACTAAGAAGCTCCGGCAAATC
>AY457914
TGATGCAGCGACGCCGCGTGAGTGAAGAAGTAATTCGTTATGTAAAGCTCTATCAGCAGGGAAGATAGAGACGGTACCTAACTAAGAAGCTCCGGCTAA
>AY457913
AGCGACGCCGCGTGAGCGAAGAAGTATTTCGGTATGTAAAGCTCTATCAGCAGGGAAGAAGAAATGACGGTACCTGACTAAGAAGCACCGGCAAATCTG
>AY457912
GCAGCGACGCCGCGTGAGTGAAGAAGTAATTCGTTATGTAAAGCTCTATCAGCAGGGAAGATAGTGACGGTACCTGACTAAGAAGCTCCGGCTAATCGT

countgaps

The countgaps parameter allows you to specify whether you want to count gaps as bases, default=false.

short

The short parameter allows you to specify you want to keep sequences that are too short to chop, default=false.

mothur > chop.seqs(fasta=abrecovery.fasta, numbases=1000, short=T)

processors

The processors option enables you to accelerate the chopping process by using multiple processors. Default processors=Autodetect number of available processors and use all available. You are able to 2 processors with the following option:

mothur > chop.seqs(fasta=abrecovery.fasta, numbases=1000, processors=2)

name && group && count

If you provide a name, group or count file any sequences removed from the fasta file will also be removed from those files.

format

The format parameter is used to indicate whether your sequences are sanger, solexa, illumina1.8+ or illumina, default=illumina1.8+.

Revisions

1.23.0 - fixed an off by one error - if you put numbases=200 the sequence come out as 199 bases.
1.27.0 - added processors option.
1.31.0 - added name, group and count options.
1.36.0 - adds qfile option to allows for chopping quality files.
1.40.0 Rewrite of threaded code. Default processors=Autodetect number of available processors and use all available.
1.47.0 Adds fastq and format parameters to chop.seqs #790