{"id":2931,"date":"2024-04-17T07:26:23","date_gmt":"2024-04-17T06:26:23","guid":{"rendered":"https:\/\/blogs.qub.ac.uk\/dipsa\/?p=2931"},"modified":"2025-04-24T05:41:10","modified_gmt":"2025-04-24T04:41:10","slug":"ms-biographs-on-ieee-dataport","status":"publish","type":"post","link":"https:\/\/blogs.qub.ac.uk\/dipsa\/ms-biographs-on-ieee-dataport\/","title":{"rendered":"MS-BioGraphs on IEEE DataPort"},"content":{"rendered":"\n

MS-BioGraph sequence similarity graph datasets are now publicly available on IEEE DataPort: https:\/\/doi.org\/10.21227\/gmd9-1534<\/a> .<\/p>\n\n\n\n

To access the files, you need to register\/login to IEEE DataPort and then visit the MS-BioGraphs page. By saving the page as an HTML file such as dp.html<\/strong><\/code>, you may download the datasets (as an example MS1<\/strong><\/code>) using the following script:<\/p>\n\n\n\n

dsname=\"MS1\"\nhtml_file=\"dp.html\"\n\nurls=`cat $html_file  | sed  -e 's\/\\&amp;\/\\&\/g'  | grep -Eo \"(http|https):\/\/[a-zA-Z0-9.\/?&=_%:-]*\" | grep amazonaws  | sort | uniq | grep -E \"$dsname[-_\\.]\"`\n\nfor u in $urls; do\n    wget $u\n    if [ $? != 0 ]; then break; fi\ndone\n\n# removing query strings\nfor f in $(find $1 -type f); do\n    if [ $f = ${f%%\\?*} ]; then continue; fi\n    mv \"${f}\" \"${f%%\\?*}\"\ndone\n\n# liking offsets.bin to be found by ParaGrapher\nln -s ${dsname}_offsets.bin ${dsname}-underlying_offsets.bin\n\n<\/code><\/pre>\n\n\n\n
Instead of wget<\/strong><\/code> you may use axel -n 10<\/strong><\/code> to use multiple connections (here, 10) for downloading each file (https:\/\/manpages.ubuntu.com\/manpages\/noble\/en\/man1\/axel.1.html<\/a>).<\/p>\n\n\n\n
MS-BioGraphs<\/a><\/strong>

Related Posts<\/strong><\/p>\n\n\n