write does not automatically append newlines

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1 Using! to tell IPython to run a shell command (in this case, I m listing the files in my working directory )!ls arraytools.py Clustering Example.ipynb clustertools.pyc Day 4.ipynb rowshuffle1.jtv rowshuffle1.um.jtv SimpleCdt.pyc supp2data.csv arraytools.pyc clustertools.py day2.txt ipython.html rowshuffle1.um.cdt SimpleCdt.py stats.py test1.cdt BMS270a ipynb clustertools.py~ day3.log rowshuffle1.cdt rowshuffle1.um.gtr SimpleCdt.py~ stats.pyc test1.jtv Parse supp2data.csv using the parser function from yesterday from clustertools import parsecsv (columns, genes, annos, logratios) = parsecsv("supp2data.csv") Retroactively starting my log %logstart -o /home/mvoorhie/projects/courses/practicalbioinformatics/python/april2013/ day4.log Activating auto-logging. Current session state plus future input saved. Filename : /home/mvoorhie/projects/courses/practicalbioinformatics/python/april2013/day4.log Mode : backup Output logging : True Raw input log : False Timestamping : False State : active Sanity check: do my arrays have the expected shape? [len(i) for i in (genes,annos,logratios)] [2467, 2467, 2467] 79 len(logratios[0])

2 -rw-rw-r-- 1 mvoorhie mvoorhie May 2 13:10 rowshuffle1.um.gtr -rw-rw-r-- 1 mvoorhie mvoorhie May 2 13:10 rowshuffle1.um.cdt -rw-rw-r-- 1 mvoorhie mvoorhie 787 May 2 13:11 rowshuffle1.um.jtv -rw-rw-r-- 1 mvoorhie mvoorhie 2464 May 2 15:07 Clustering Example.ipynb -rw-rw-r-- 1 mvoorhie mvoorhie 2451 May 2 15:08 Day 4.ipynb -rw-rw-r-- 1 mvoorhie mvoorhie 0 May 2 15:22 test.cdt -rw-rw-r-- 1 mvoorhie mvoorhie 596 May 2 15:23 day4.log fp2 = open("test1.jtv","w")!ls -lrt tail -rw-rw-r-- 1 mvoorhie mvoorhie May 2 13:09 rowshuffle1.cdt -rw-rw-r-- 1 mvoorhie mvoorhie 717 May 2 13:09 rowshuffle1.jtv -rw-rw-r-- 1 mvoorhie mvoorhie May 2 13:10 rowshuffle1.um.gtr -rw-rw-r-- 1 mvoorhie mvoorhie May 2 13:10 rowshuffle1.um.cdt -rw-rw-r-- 1 mvoorhie mvoorhie 787 May 2 13:11 rowshuffle1.um.jtv -rw-rw-r-- 1 mvoorhie mvoorhie 2464 May 2 15:07 Clustering Example.ipynb -rw-rw-r-- 1 mvoorhie mvoorhie 2451 May 2 15:08 Day 4.ipynb -rw-rw-r-- 1 mvoorhie mvoorhie 0 May 2 15:22 test.cdt -rw-rw-r-- 1 mvoorhie mvoorhie 0 May 2 15:27 test1.jtv -rw-rw-r-- 1 mvoorhie mvoorhie 664 May 2 15:27 day4.log write does not automatically append newlines fp.write("this is the first line") fp.write("this is the second line") fp.close() fp = open("test.cdt") fp.readline() this is the first linethis is the second line fp.close() fp = open("test.cdt","w") fp.write("this is the first line\n") fp.write("this is the second line\n") fp.close() fp = open("test.cdt") fp.readline() this is the first line\n 2

3 Digression: making function parameters optional by giving them default values def f(x, y = 2): print x, y f(3) 3 2 f(4, 5) 4 5 def f(x, y =2,z=3): print x,y,z f(3) f(2,4) f(2, z = 66) def f(x, *args, **kw): print x print kw["z"] f(3, z = 17) 3 17 Back to figuring out how to format my arrays for output genes[:10] [ YBR166C, YOR357C, YLR292C, YGL112C, YIL118W, YDL120W, YHL025W, YGL248W, YIL146C, 3

4 YJR106W ] ",".join(genes[:10]) YBR166C,YOR357C,YLR292C,YGL112C,YIL118W,YDL120W,YHL025W,YGL248W,YIL146C,YJR106W "asdfasdf".join(genes[:10]) YBR166CasdfasdfYOR357CasdfasdfYLR292CasdfasdfYGL112CasdfasdfYIL118WasdfasdfYDL120WasdfasdfYHL025Wasdfas "\t".join(genes[:10]) YBR166C\tYOR357C\tYLR292C\tYGL112C\tYIL118W\tYDL120W\tYHL025W\tYGL248W\tYIL146C\tYJR106W print "\t".join(genes[:10]) YBR166C YOR357C YLR292C YGL112C YIL118W YDL120W YHL025W YGL248W YIL146C YJR106W "\t".join(logratios[0][:10]) TypeError Traceback (most recent call last) <ipython-input-37-e3d72ab96daf> in <module>() ----> 1 "\t".join(logratios[0][:10]) TypeError: sequence item 0: expected string, float found str(3.5) 3.5 p = pi p = str(p) Mad-libbing strings (string substitution) "%s" % p

5 "The %s dog jumped over the %s fox" % ("quick","lazy") The quick dog jumped over the lazy fox "The %s dog jumped over the %s fox" % (p,"lazy") The dog jumped over the lazy fox "The %.3f dog jumped over the %s fox" % (p,"lazy") The dog jumped over the lazy fox "The %e dog jumped over the %s fox" % (p,"lazy") The e+00 dog jumped over the lazy fox fp = open("test.cdt","w") fp.write("\t".join(["uniqid","name"]+[str(i) for i in range(79)])+"\n") x = "asdfasdf" x += "asdfasdf" x asdfasdfasdfasdf "asdfasdf"+"asdfasdf" asdfasdfasdfasdf Lists vs. list comprehensions vs. generator expressions # simple list [1,2,3,] [1, 2, 3] # list comprehension [i**2 for i in range(10)] [0, 1, 4, 9, 16, 25, 36, 49, 64, 81] ",".join(["2343","2342"]) 5

6 2343,2342 ",".join(["2343","2342"]+["hi" for i in range(5)]) 2343,2342,hi,hi,hi,hi,hi # generator expression x = (i**2 for i in range(10)) x <generator object <genexpr> at 0x428daa0> 0 x.next() 1 x.next() for i in x: print i A working version of the output function that we were working on today (see SimpleCdt.py on the website for a different version) def pretty(f): if(f is None): return "" else: return str(f) def writecdt(genes, annos, logratios, fname): fp = open(fname,"w") fp.write("\t".join(["uniqid","name"]+[str(i) for i in xrange(len(logratios[0]))])+"\n ") for (gene, anno, ratio) in zip(genes, annos, logratios): fp.write("\t".join([gene,anno]+[pretty(i) for i in ratio])+"\n") 6

7 fp.close() writecdt(genes, annos, logratios, "test1.cdt") str(none) None Here I m launching javatreeview with a convenience script you can start JavaTreeView from the Start menu on windows or the Applications folder on OS X!javatreeview.sh test1.cdt created xml config from file /home/mvoorhie/.javatreeviewxmlrc Plugin Jar jar:file:/home/mvoorhie/cpackages/javatreeview/alok-git/jtreeview/linkedview/dist/plugins/den Registering Plugin Dendrogram Registering Plugin Alignment Registering Plugin KnnDendrogram Plugin Jar jar:file:/home/mvoorhie/cpackages/javatreeview/alok-git/jtreeview/linkedview/dist/plugins/kar Registering Plugin Karyoscope Plugin Jar jar:file:/home/mvoorhie/cpackages/javatreeview/alok-git/jtreeview/linkedview/dist/plugins/tre Registering Plugin ArrayTreeAnno Registering Plugin GeneTreeAnno Plugin Jar jar:file:/home/mvoorhie/cpackages/javatreeview/alok-git/jtreeview/linkedview/dist/plugins/sca Registering Plugin Scatterplot loading /home/mvoorhie/projects/courses/practicalbioinformatics/python/april2013/test1.cdt... Finding Cdt Dimensions loading Array Annotations loading Gene Annotations Parsing strings into doubles... parsing jtv config file created xml config from file /home/mvoorhie/projects/courses/practicalbioinformatics/python/april2013/te final style classic showing popup... Successfully stored config file /home/mvoorhie/projects/courses/practicalbioinformatics/python/april2013 Successfully stored config file /home/mvoorhie/projects/courses/practicalbioinformatics/python/april2013 Successfully stored config file /home/mvoorhie/projects/courses/practicalbioinformatics/python/april2013 Successfully stored config file /home/mvoorhie/.javatreeviewxmlrc Successfully stored config file /home/mvoorhie/projects/courses/practicalbioinformatics/python/april2013 ViewFrame.dispose 7

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