06-11-2009
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Making an information matrix using Java
Hello all,
I'm doing some research in Biostatistics this summer studying chloroplast genomes. I have 19 text files that look exactly like this:
Name: Marchantia polymorpha
FileName: NC_001319
Bases: 121024
Genes: rps12 <85..842
rps7 (892..1359)
ndhB (1514..3555)
psbM (4001..4105)
rpoB (5859..9056)
rpoC1 (9087..11737)
rpoC2 (11811..15971)
rps2 (16055..16762)
atpI (16890..17636)
atpH (18014..18259)
atpF (18468..19609)
atpA (19654..21177)
ycf12 -(22162..22263)
psbI -(22997..23107)
psbK -(23438..23605)
chlB (24053..25594)
psbA (28368..29429)
mbpX (37012..38124)
psbD (38855..39916)
psbC (39864..41285)
psbZ (41647..41835)
rps14 -(42333..42635)
psaB -(42724..44928)
psaA -(44955..47207)
rps4 -(49425..50033)
ndhJ -(51233..51709)
ndhK -(51793..52524)
ndhC -(52515..52877)
atpE -(53955..54362)
atpB -(54368..55846)
rbcL (56355..57782)
accD (58065..59015)
psaI (59193..59303)
ycf4 (59525..60079)
cemA (60151..61455)
petA (61641..62603)
psbJ -(62794..62916)
psbL -(63036..63152)
psbF -(63174..63293)
psbE -(63303..63554)
petG (64370..64483)
psaJ (65027..65155)
rpl33 (65273..65470)
rps18 (65498..65725)
rpl20 -(65807..66157)
clpP -(67130..68640)
psbB (69026..70552)
psbT (70669..70776)
psbN -(70863..70994)
psbH (71092..71316)
petB (71424..72566)
petD (72715..73690)
rpoA -(73802..74824)
rps11 -(74857..75249)
rpl36 -(75300..75413)
infA -(75450..75686)
rps8 -(75773..76171)
rpl14 -(76253..76621)
rpl16 -(76719..77685)
rps3 -(77743..78396)
rpl22 -(78445..78804)
rps19 -(78822..79100)
rpl2 -(79137..80514)
rpl23 -(80550..80825)
ndhF -(91101..93179)
rpl21 (93469..93819)
rpl32 (93886..94095)
cysT (94183..95049)
ccsA (95482..96444)
ndhD -(96665..98164)
psaC -(98289..98534)
ndhE -(98757..99059)
ndhG -(99113..99688)
ndhI -(99779..100330)
ndhA -(100382..102200)
ndhH -(102202..103380)
rps15 -(103433..103699)
chlL -(110104..110973)
Of course, each one of the 19 files have a different Name, NC_ number, number of bases, and different genes in different numerical positions. I have a slight knowledge of Java, and wish to take these files and make an information matrix. The NC_ numbers of the 19 different genes would be listed across the top, and each gene would be listed down the side. Then, in a matrix, if that NC_ number file contains a certain gene on the left, place a 1 in the matrix, otherwise a 0. If I just have the 19 text files as command line args, is it possible to do this somehow? Maybe with a TreeMap or other data structure?
If it would make it easier, I could also trim the files down to just the gene names, with the headings of the numerical positions next to each. I don't really know what would be best, but some program that could make this matrix would really help my research. Thanks to anyone taking the time to read this and any ideas would help!
-akreibich07
