Interproscan, xml文件转化为tsv

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将interproscan的结果转化格式

很奇怪 tsv格式里没有go, kegg, inter-domain信息，但是xml文件里面却有，tsv文件比较好处理，所以先将xml文件转化为tsv。用软件自带的工具:

The convert mode is designed to work only for XML documents created with the same version. This makes sure we can introduce new schema updates in the future. However the XML schema is stable and will only change, if we need to add new features for instance.

You can use InterProScan 5‘s CONVERT mode to reformat your XML result file into any other possible output format (TSV, GFF3, SVG and HTML). For compatibility reasons you can also convert XML results into InterProScan 4.8 raw format. This will give our users enough time to migrate their pipeline to InterProScan 5.

Please note it is NOT possible to reformat any non-XML format. XML is the richest data type and is therefore the only format which allows us to produce any other format of interest.

To enable InterProScan 5 to run in CONVERT mode you need to set the mode option to ‘CONVERT‘.

Usage instructions

./interproscan.sh -mode convert

You will see the following usage instructions:

Welcome to InterProScan v5 CONVERT mode.
usage: java -XX:+UseParallelGC -XX:+AggressiveOpts
            -XX:+UseFastAccessorMethods -Xms512M -Xmx2048M -jar
            interproscan-5.jar

Please give us your feedback by sending an email to
interhelp@ebi.ac.uk
 -b,--output-file-base <OUTPUT-FILE-BASE>   Optional, base output
                                            filename.  Note that this
                                            option and the --outfile (-o)
                                            option are mutually exclusive.
                                            The appropriate file extension
                                            for the output format(s) will
                                            be appended automatically. By
                                            default the input file
                                            path/name will be used.

 -d,--output-dir <OUTPUT-DIR>               Optional, output directory.
                                            Note that this option and the
                                            --outfile (-o) option or the
                                            --output-file-base (-b) option
                                            are mutually exclusive. The
                                            appropriate file extension for
                                            the output format(s) will be
                                            appended automatically. By
                                            default the input file
                                            path/name will be used.

 -f,--formats <OUTPUT-FORMATS>              Optional, case-insensitive,
                                            comma separated list of output
                                            formats. Available formats are
                                            TSV, GFF3 (default set) and
                                            RAW (InterProScan 4 TSV),
                                            HTML, SVG.

 -i,--xml <XML-FILE-PATH>                   Mandatory, path to the IMPACT
                                            XML file that should be loaded
                                            and converted.

 -o,--outfile <EXPLICIT_OUTPUT_FILENAME>    Optional explicit output file
                                            name.  Note that this option
                                            and the --output-file-base
                                            (-b) option are mutually
                                            exclusive. If this option is
                                            given, you MUST specify a
                                            single output format using the
                                            -f option.  The output file
                                            name will not be modified.
                                            Note that specifying an output
                                            file name using this option
                                            OVERWRITES ANY EXISTING FILE.

 -T,--tempdir <TEMP-DIR>                    Optional, specify temporary
                                            file directory. The default
                                            location is /temp.

具体使用：

/share/bioinfo/miaochenyong/interproscan-software/tars/interproscan-5.7-48.0/interproscan.sh -mode convert -f tsv -i your_xml_file
如果输入文件为test.xml

默认输出文件为：test.xml.tsv

by freemao

FAFU

Interproscan, xml文件转化为tsv

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原文地址：http://www.cnblogs.com/freemao/p/4932024.html