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| Original file line number | Diff line number | Diff line change |
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@@ -119,7 +119,7 @@ Usage | |
| ``` | ||
| fakit -- a cross-platform and efficient suit for FASTA/Q file manipulation | ||
| Version: 0.2.3 | ||
| Version: 0.2.4 | ||
| Author: Wei Shen <[email protected]> | ||
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@@ -134,7 +134,8 @@ Available Commands: | |
| faidx create FASTA index file | ||
| fq2fa covert FASTQ to FASTA | ||
| fx2tab covert FASTA/Q to tabular format (with length/GC content/GC skew) | ||
| grep search sequences by pattern(s) of name or sequence motifs | ||
| grep search sequences by pattern(s) of name or sequence motifss | ||
| head print first N FASTA/Q records | ||
| locate locate subsequences/motifs | ||
| rename rename duplicated IDs | ||
| replace replace name/sequence/by regular expression | ||
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@@ -960,6 +961,12 @@ Flags: | |
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| Examples | ||
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| 1. Sample by proportion | ||
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| $ zcat hairpin.fa.gz | fakit sample -p 0.1 -o sample.fa.gz | ||
| [INFO] sample by proportion | ||
| [INFO] 2814 sequences outputed | ||
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| 1. Sample by number | ||
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| $ zcat hairpin.fa.gz | fakit sample -n 1000 -o sample.fa.gz | ||
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@@ -968,11 +975,9 @@ Examples | |
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| ***To reduce memory usage when spliting big file, we could use flag `--two-pass`*** | ||
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| 1. Sample by proportion | ||
| ***We can also use `fakit sample -p` followed with `fakit head -n`:*** | ||
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| $ zcat hairpin.fa.gz | fakit sample -p 0.1 -o sample.fa.gz | ||
| [INFO] sample by proportion | ||
| [INFO] 2814 sequences outputed | ||
| $ zcat hairpin.fa.gz | fakit sample -p 0.1 | fakit head -n 1000 -o sample.fa.gz | ||
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| 1. Set rand seed to reproduce the result | ||
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@@ -985,6 +990,46 @@ Examples | |
| Note that when sampling on FASTQ files, make sure using same random seed by | ||
| flag `-s` (`--rand-seed`) | ||
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| ## head | ||
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| Usage | ||
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| ``` | ||
| print first N FASTA/Q records | ||
| Usage: | ||
| fakit head [flags] | ||
| Flags: | ||
| -n, --number int print first N FASTA/Q records (default 10) | ||
| ``` | ||
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| Examples | ||
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| 1. FASTA | ||
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| $ fakit head -n 1 hairpin.fa.gz | ||
| >cel-let-7 MI0000001 Caenorhabditis elegans let-7 stem-loop | ||
| UACACUGUGGAUCCGGUGAGGUAGUAGGUUGUAUAGUUUGGAAUAUUACCACCGGUGAAC | ||
| UAUGCAAUUUUCUACCUUACCGGAGACAGAACUCUUCGA | ||
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| 1. FASTQ | ||
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| $ fakit head -n 1 reads_1.fq.gz | ||
| @HWI-D00523:240:HF3WGBCXX:1:1101:2574:2226 1:N:0:CTGTAG | ||
| TGAGGAATATTGGTCAATGGGCGCGAGCCTGAACCAGCCAAGTAGCGTGAAGGATGACTG | ||
| CCCTACGGGTTGTAAACTTCTTTTATAAAGGAATAAAGTGAGGCACGTGTGCCTTTTTGT | ||
| ATGTACTTTATGAATAAGGATCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGA | ||
| TCCGAGCGTTATCCGGATTTATTGGGTTTAAAGGGTGCGCAGGCGGT | ||
| + | ||
| HIHIIIIIHIIHGHHIHHIIIIIIIIIIIIIIIHHIIIIIHHIHIIIIIGIHIIIIHHHH | ||
| HHGHIHIIIIIIIIIIIGHIIIIIGHIIIIHIIHIHHIIIIHIHHIIIIIIIGIIIIIII | ||
| HIIIIIGHIIIIHIIIH?DGHEEGHIIIIIIIIIIIHIIHIIIHHIIHIHHIHCHHIIHG | ||
| IHHHHHHH<GG?B@EHDE-BEHHHII5B@GHHF?CGEHHHDHIHIIH | ||
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| ## replace | ||
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| Usage | ||
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Submodule site
updated
from 006cf5 to 24341f
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,83 @@ | ||
| // Copyright © 2016 Wei Shen <[email protected]> | ||
| // | ||
| // Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| // of this software and associated documentation files (the "Software"), to deal | ||
| // in the Software without restriction, including without limitation the rights | ||
| // to use, copy, modify, merge, publish, distribute, sublicense, and/or sell | ||
| // copies of the Software, and to permit persons to whom the Software is | ||
| // furnished to do so, subject to the following conditions: | ||
| // | ||
| // The above copyright notice and this permission notice shall be included in | ||
| // all copies or substantial portions of the Software. | ||
| // | ||
| // THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| // IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| // FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE | ||
| // AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| // LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, | ||
| // OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN | ||
| // THE SOFTWARE. | ||
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| package cmd | ||
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| import ( | ||
| "runtime" | ||
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| "github.com/brentp/xopen" | ||
| "github.com/shenwei356/bio/seq" | ||
| "github.com/shenwei356/bio/seqio/fastx" | ||
| "github.com/spf13/cobra" | ||
| ) | ||
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| // headCmd represents the head command | ||
| var headCmd = &cobra.Command{ | ||
| Use: "head", | ||
| Short: "print first N FASTA/Q records", | ||
| Long: `print first N FASTA/Q records | ||
| `, | ||
| Run: func(cmd *cobra.Command, args []string) { | ||
| config := getConfigs(cmd) | ||
| alphabet := config.Alphabet | ||
| idRegexp := config.IDRegexp | ||
| chunkSize := config.ChunkSize | ||
| bufferSize := config.BufferSize | ||
| lineWidth := config.LineWidth | ||
| outFile := config.OutFile | ||
| seq.AlphabetGuessSeqLenghtThreshold = config.AlphabetGuessSeqLength | ||
| seq.ValidateSeq = false | ||
| runtime.GOMAXPROCS(config.Threads) | ||
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| number := getFlagPositiveInt(cmd, "number") | ||
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| files := getFileList(args) | ||
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| outfh, err := xopen.Wopen(outFile) | ||
| checkError(err) | ||
| defer outfh.Close() | ||
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| i := 0 | ||
| for _, file := range files { | ||
| fastxReader, err := fastx.NewReader(alphabet, file, bufferSize, chunkSize, idRegexp) | ||
| checkError(err) | ||
| for chunk := range fastxReader.Ch { | ||
| checkError(chunk.Err) | ||
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| for _, record := range chunk.Data { | ||
| i++ | ||
| record.FormatToWriter(outfh, lineWidth) | ||
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| if number == i { | ||
| fastxReader.Cancel() | ||
| return | ||
| } | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| } | ||
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| func init() { | ||
| RootCmd.AddCommand(headCmd) | ||
| headCmd.Flags().IntP("number", "n", 10, "print first N FASTA/Q records") | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -32,10 +32,10 @@ import ( | |
| // RootCmd represents the base command when called without any subcommands | ||
| var RootCmd = &cobra.Command{ | ||
| Use: "fakit", | ||
| Short: "a cross-platform and efficient suit for FASTA/Q file manipulation", | ||
| Long: `fakit -- a cross-platform and efficient suit for FASTA/Q file manipulation | ||
| Short: "a cross-platform and efficient toolkit for FASTA/Q file manipulation", | ||
| Long: `fakit -- a cross-platform and efficient toolkit for FASTA/Q file manipulation | ||
| Version: 0.2.3 | ||
| Version: 0.2.4 | ||
| Author: Wei Shen <[email protected]> | ||
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