fasta_filter: Filter a fasta file
In vaulot/dvutils: A set of utilities
Description
Usage
Arguments
Value
To do
Examples
Description
Read a fasta file and write back a fasta file keeping only sequences with less than max_ambig and between min and max length.
The file name is changed from xxx.fas to xxx.filtered.fas.
Prints also the number of sequences in and out.
Usage
1
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fasta_filter(
file_name,
min_length = 100,
max_length = 10000,
type = "AA",
max_ambig = 5
)
Arguments
file_name
Name the input fasta file
min_length
Minimum length of sequences to keep
max_length
Maximum length of sequences to keep
type
"DNA" or "AA"
max_ambig
Maximum number of ambiguites
Value
TRUE if it terminates OK
To do
Nothing =)
Examples
1
fasta_filter("protein.faa", min_length=100, max_length=10000, type="AA", max_ambig=5)
vaulot/dvutils documentation built on Nov. 20, 2021, 11:01 a.m.
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Description Usage Arguments Value To do Examples
Description
Read a fasta file and write back a fasta file keeping only sequences with less than max_ambig and between min and max length. The file name is changed from xxx.fas to xxx.filtered.fas. Prints also the number of sequences in and out.
Usage
1 2 3 4 5 6 7 | fasta_filter(
file_name,
min_length = 100,
max_length = 10000,
type = "AA",
max_ambig = 5
)
|
Arguments
file_name |
Name the input fasta file |
min_length |
Minimum length of sequences to keep |
max_length |
Maximum length of sequences to keep |
type |
"DNA" or "AA" |
max_ambig |
Maximum number of ambiguites |
Value
TRUE if it terminates OK
To do
Nothing =)
Examples
1 | fasta_filter("protein.faa", min_length=100, max_length=10000, type="AA", max_ambig=5)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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