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faidx - Online in the Cloud

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This is the command faidx that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

NAME


faidx - Fetch sequences from FASTA

SYNOPSIS


faidx [-h] [-b BED] [-o OUT] [-i {bed,chromsizes,nucleotide,transposed}] [-c] [-r] [-n |
-f] [-x] [-l] [-s DEFAULT_SEQ] [-d DELIMITER] [-g REGEX] [-m | -M] [--version] fasta
[regions [regions ...]]

DESCRIPTION


Fetch sequences from FASTA. If no regions are specified, all entries in the input file are
returned. Input FASTA file must be consistently line-wrapped, and line wrapping of output
is based on input line lengths.

OPTIONS


Positional arguments
fasta FASTA file

regions
space separated regions of sequence to fetch e.g. chr1:1-1000

Optional arguments
-h, --help
show this help message and exit

-b BED, --bed BED
bed file of regions

-o OUT, --out OUT
output file name (default: stdout)

-i {bed,chromsizes,nucleotide,transposed}, --transform
{bed,chromsizes,nucleotide,transposed}
transform the requested regions into another format. default: None

-c, --complement
complement the sequence. default: False

-r, --reverse
reverse the sequence. default: False

-n, --no-names
omit sequence names from output. default: False

-f, --full-names
output full names including description. default: False

-x, --split-files
write each region to a separate file (names are derived from regions)

-l, --lazy
fill in --default-seq for missing ranges. default: False

-s DEFAULT_SEQ, --default-seq DEFAULT_SEQ
default base for missing positions and masking. default: N

-d DELIMITER, --delimiter DELIMITER
delimiter for splitting names to multiple values (duplicate names will be
discarded). default: None

-g REGEX, --regex REGEX
regular expression for filtering non-matching sequence names. default: .*

-m, --mask-with-default-seq
mask the FASTA file using --default-seq default: False

-M, --mask-by-case
mask the FASTA file by changing to lowercase. default: False

--version
print pyfaidx version number

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