Read unusually formatted CSV data.
This means being able to process CSV data with peculiar quoting rules
using --quote or --no-quoting, or dealing with character escaping, typically
files with backslash escaping, with --escape.
This command is also able to skip metadata headers sometimes found at the beginning
of CSV-adjacent formats with the -L/--skip-lines, -U/--skip-until & -W/--skip-while
flags.
Finally you can also use this command to handle compressed streams and well-known
CSV-adjacent format streams (note that it is not necessary to use `xan input` if
the file is already on disk and has the expected extension, as xan knows how
to deal with some of those formats out-of-the-box). A notable exception to this is
GFF files that require `xan input` to be read.
Usage:
xan input [options] [<input>]
formatting options:
--tabs Same as -d '\t', i.e. use tabulations as delimiter.
--quote <char> The quote character to use. [default: "]
--escape <char> The escape character to use. When not specified,
quotes are escaped by doubling them.
--no-quoting Disable quoting completely.
--comment <char> Skip records starting with this character.
--trim Whether to trim cell values.
header skipping options:
-L, --skip-lines <n> Skip the first <n> lines of the file.
-U, --skip-until <pattern> Skip lines until <pattern> matches.
-W, --skip-while <pattern> Skip lines while <pattern> matches.
CSV-adjacent data format options:
--vcf Indicate that the given stream should be understood as a VCF ("Variant Call Format")
file from bioinformatics. This is not needed when using xan on a file
with `.vcf` extension because xan already knows how to handle them.
https://en.wikipedia.org/wiki/Variant_Call_Format
--gtf Indicate that the given stream should be understood as a GTF ("Gene Transfer Format")
file from bioinformatics. This is not needed when using xan on a file
with `.gtf` or `.gff2` extension because xan already knows how to handle them.
https://en.wikipedia.org/wiki/Gene_transfer_format
--gff Indicate that the given stream should be understood as a GFF ("General Feature Format")
file from bioinformatics. This flag is implied if target file has
the `.gff` or `.gff3` extension.
https://en.wikipedia.org/wiki/General_feature_format
--sam Indicate that the given stream should be understood as a SAM ("Sequence Alignment Map")
file from bioinformatics. This is not needed when using xan on a file
with `.sam` extension because xan already knows how to handle them.
https://en.wikipedia.org/wiki/SAM_(file_format)
--bed Indicate that the given stream should be understood as a BED ("Browser Extensible Data")
file from bioinformatics. This is not needed when using xan on a file
with `.bed` extension because xan already knows how to handle them.
Note that the file will be considered as tab-delimited, not space-delimited!
https://en.wikipedia.org/wiki/BED_(file_format)
--cdx Indicate that the given stream should be understood as a CDX index
file from web archives. This is not needed when using xan on a file
with `.cdx` extension because xan already knows how to handle them.
https://iipc.github.io/warc-specifications/specifications/cdx-format/cdx-2015/
compression options:
--gzip Read a gzip-compressed stream or gzip-compressed file without the
standard `.gz` extension.
--zstd Read a zstd-compressed stream or zstd-compressed file without the
standard `.zst` extension.
Common options:
-h, --help Display this message
-o, --output <file> Write output to <file> instead of stdout.
-d, --delimiter <arg> The field delimiter for reading CSV data.
Must be a single character.