|
|
| | Checked with Expasy translation tool. | | Checked with Expasy translation tool. |
| | | | |
| − | For the XMLPipeDB utility I used the wiki provided on the course website. The first command I found on the wiki after scrolling down to the "Running Command-Line Java Programs" section. I entered the commands into the command prompt window under the directory, ~dondi/xmlpipedb/data, this allowed me to use the XMLPipeDB utitlity. | + | For the XMLPipeDB utility I used the wiki provided on the course website. The first command I found on the wiki after scrolling down to the "Running Command-Line Java Programs" section. I entered the commands into the command prompt window under the directory, ~dondi/xmlpipedb/data, this allowed me to use the XMLPipeDB utility. |
| | | | |
| | === XMLPipeDB Match Practice === | | === XMLPipeDB Match Practice === |
|
|
| | | | |
| | # What Match command tallies the occurrences of the pattern <code>GO:000[567]</code> in the ''493.P_falciparum.xml'' file? | | # What Match command tallies the occurrences of the pattern <code>GO:000[567]</code> in the ''493.P_falciparum.xml'' file? |
| | + | #*Using the wiki page I found this command and ran it in ~dondi/xmlpipedb/data |
| | #*java -jar xmlpipedb-match-1.1.1.jar GO:000[567] < 493.P_falciparum.xml | | #*java -jar xmlpipedb-match-1.1.1.jar GO:000[567] < 493.P_falciparum.xml |
| | #* How many unique matches are there? | | #* How many unique matches are there? |
| | + | #*I read the output of the function, and wrote it here. |
| | #**Total Unique Matches: 3 | | #**Total Unique Matches: 3 |
| | #* How many times does each unique match appear? | | #* How many times does each unique match appear? |
| | + | #**More reading of output brought me to this spot, and I wrote it down after clicking on "edit" on this wiki page. |
| | #**go:0007: 113 | | #**go:0007: 113 |
| | #**go:0006: 1100 | | #**go:0006: 1100 |
| | #**go:0005: 1371 | | #**go:0005: 1371 |
| | # Try to find one such occurrence “in situ” within that file. Look at the neighboring content around that occurrence. | | # Try to find one such occurrence “in situ” within that file. Look at the neighboring content around that occurrence. |
| | + | #*One such occurrence: <dbReference type="GO" id="GO:0005777"> |
| | #* Describe how you did this. | | #* Describe how you did this. |
| | + | #**I entered grep "GO:000[567]" 493.P_falciparum.xml | more, as a command and then picked out a random occurrence. I then edited the wiki page and wrote it down. |
| | #* Based on where you find this occurrence, what kind of information does this pattern represent? | | #* Based on where you find this occurrence, what kind of information does this pattern represent? |
| | + | #**The ID of the gene ontology within a database, or an identifier of a gene ontology term. I found this out on the match utility wiki page. |
| | # What Match command tallies the occurrences of the pattern <code>\"Yu.*\"</code> in the ''493.P_falciparum.xml'' file? | | # What Match command tallies the occurrences of the pattern <code>\"Yu.*\"</code> in the ''493.P_falciparum.xml'' file? |
| | + | #* Entered this command into terminal, have not changed directories. |
| | #*java -jar xmlpipedb-match-1.1.1.jar \"Yu.*\" < 493.P_falciparum.xml | | #*java -jar xmlpipedb-match-1.1.1.jar \"Yu.*\" < 493.P_falciparum.xml |
| | #* How many unique matches are there? | | #* How many unique matches are there? |
| | + | #** Read output and jotted it down here. |
| | #**3 | | #**3 |
| | #* How many times does each unique match appear? | | #* How many times does each unique match appear? |
|
|
| | #**Total unique matches: 1 | | #**Total unique matches: 1 |
| | #* What answer does '''grep''' + '''wc''' give you? | | #* What answer does '''grep''' + '''wc''' give you? |
Exception encountered, of type "Error"
[db563d2b] /biodb/fall2015/index.php?diff=1504&oldid=1488&title=Jwoodlee_Week_3 Error from line 434 of /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php: Call to undefined function each()
Backtrace:
#0 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(544): DiffEngine->diag()
#1 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(344): DiffEngine->compareSeq()
#2 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(227): DiffEngine->diffLocal()
#3 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(721): DiffEngine->diff()
#4 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(859): Diff->__construct()
#5 /apps/xmlpipedb/biodb/fall2015/includes/diff/DairikiDiff.php(980): MappedDiff->__construct()
#6 /apps/xmlpipedb/biodb/fall2015/includes/diff/TableDiffFormatter.php(194): WordLevelDiff->__construct()
#7 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(140): TableDiffFormatter->changed()
#8 /apps/xmlpipedb/biodb/fall2015/includes/diff/DiffFormatter.php(111): DiffFormatter->block()
#9 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(888): DiffFormatter->format()
#10 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(802): DifferenceEngine->generateTextDiffBody()
#11 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(733): DifferenceEngine->generateContentDiffBody()
#12 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(662): DifferenceEngine->getDiffBody()
#13 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(632): DifferenceEngine->getDiff()
#14 /apps/xmlpipedb/biodb/fall2015/includes/diff/DifferenceEngine.php(453): DifferenceEngine->showDiff()
#15 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(795): DifferenceEngine->showDiffPage()
#16 /apps/xmlpipedb/biodb/fall2015/includes/page/Article.php(506): Article->showDiffPage()
#17 /apps/xmlpipedb/biodb/fall2015/includes/actions/ViewAction.php(44): Article->view()
#18 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(395): ViewAction->show()
#19 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(273): MediaWiki->performAction()
#20 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(566): MediaWiki->performRequest()
#21 /apps/xmlpipedb/biodb/fall2015/includes/MediaWiki.php(414): MediaWiki->main()
#22 /apps/xmlpipedb/biodb/fall2015/index.php(44): MediaWiki->run()
#23 {main}