Zip
並行讀取壓縮文件的內容而不提取
我有以下 zip 存檔結構：
$ unzip -l Undetermined_S0_L004_R1_001_fastqc.zip Archive: Undetermined_S0_L004_R1_001_fastqc.zip Length Date Time Name -------- ---- ---- ---- 0 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/ 0 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Icons/ 0 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/ 1197 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Icons/fastqc_icon.png 1450 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Icons/warning.png 1561 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Icons/error.png 1715 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Icons/tick.png 782 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/summary.txt 9095 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/per_base_quality.png 14381 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/per_tile_quality.png 23205 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/per_sequence_quality.png 30978 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/per_base_sequence_content.png 31152 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/per_sequence_gc_content.png 7861 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/per_base_n_content.png 18356 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/sequence_length_distribution.png 23040 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/duplication_levels.png 9096 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/adapter_content.png 58683 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/Images/kmer_profiles.png 355919 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/fastqc_report.html 301092 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/fastqc_data.txt 10117 10-10-14 14:44 Undetermined_S0_L004_R1_001_fastqc/fastqc.fo -------- ------- 899680 21 files怎麼可能並行使用
fastqc_data.txt，crimson因為目前我收到以下錯誤：find `pwd`/*_fastqc.zip -type f | parallel -j 3 unzip -c {} {}/fastqc_data.txt | crimson fastqc {} | less Usage: crimson fastqc [OPTIONS] INPUT [OUTPUT] Error: Invalid value for "input": Path "{}" does not exist.
您有一個由四個命令組成的管道：
find，其中列出了 zip 文件。parallel，它呼叫unzip以在每個 zip 文件中提取一個文件。鑑於它{}被 zip 文件的路徑替換，您嘗試home/user977828/stuff/Undetermined_S0_L004_R1_001_fastqc.zip/fastqc_data.txt從存檔中提取文件（如果目前目錄是/home/user977828/stuff）。crimson，它接收標準輸入上提取的文件的混亂，並使用參數fastqc和呼叫{}，less.
parallel``{}僅在其論點中替換。它不能對管道的其他部分做任何事情。如果要單獨呼叫crimson每個fastqc_data.txt文件，則需要將管道從unziptocrimson作為參數傳遞給parallel.find *_fastqc.zip -type f | sed 's/\.zip$//' | parallel -j 3 'unzip -c {}.zip {}/fastqc_data.txt | crimson fastqc /dev/stdin' | less