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@@ -172,7 +172,7 @@ reproduced in different environments with same random seed. | |
| ``` text | ||
| SeqKit -- a cross-platform and ultrafast toolkit for FASTA/Q file manipulation | ||
| Version: 0.11.0 | ||
| Version: 0.12.0 | ||
| Author: Wei Shen <[email protected]> | ||
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@@ -225,7 +225,7 @@ Flags: | |
| -h, --help help for seqkit | ||
| --id-ncbi FASTA head is NCBI-style, e.g. >gi|110645304|ref|NC_002516.2| Pseud... | ||
| --id-regexp string regular expression for parsing ID (default "^(\\S+)\\s?") | ||
| --infile-list string file of input files list (one file per line), if given, files from cli arguments are ignored | ||
| --infile-list string file of input files list (one file per line), if given, they are appended to files from cli arguments | ||
| -w, --line-width int line width when outputing FASTA format (0 for no wrap) (default 60) | ||
| -o, --out-file string out file ("-" for stdout, suffix .gz for gzipped out) (default "-") | ||
| --quiet be quiet and do not show extra information | ||
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@@ -281,7 +281,7 @@ Usage: | |
| seqkit seq [flags] | ||
| Flags: | ||
| -p, --complement complement sequence (blank for Protein sequence) | ||
| -p, --complement complement sequence, flag '-v' is recommended to switch on | ||
| --dna2rna DNA to RNA | ||
| -G, --gap-letters string gap letters (default "- \t.") | ||
| -h, --help help for seq | ||
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@@ -301,16 +301,6 @@ Flags: | |
| -u, --upper-case print sequences in upper case | ||
| -v, --validate-seq validate bases according to the alphabet | ||
| -V, --validate-seq-length int length of sequence to validate (0 for whole seq) (default 10000) | ||
| Global Flags: | ||
| --alphabet-guess-seq-length int length of sequence prefix of the first FASTA record based on which seqkit guesses the sequence type (0 for whole seq) (default 10000) | ||
| --id-ncbi FASTA head is NCBI-style, e.g. >gi|110645304|ref|NC_002516.2| Pseud... | ||
| --id-regexp string regular expression for parsing ID (default "^(\\S+)\\s?") | ||
| -w, --line-width int line width when outputing FASTA format (0 for no wrap) (default 60) | ||
| -o, --out-file string out file ("-" for stdout, suffix .gz for gzipped out) (default "-") | ||
| --quiet be quiet and do not show extra information | ||
| -t, --seq-type string sequence type (dna|rna|protein|unlimit|auto) (for auto, it automatically detect by the first sequence) (default "auto") | ||
| -j, --threads int number of CPUs. (default value: 1 for single-CPU PC, 2 for others) (default 2) | ||
| ``` | ||
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| Examples | ||
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