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In [1]:
ls /mnt
evokerr/   hljordt/     mherrmannsfeldt/      titus/
foenpeng/  lnj204/      qchrist2/             titus2/
haoran/    lost+found/  SRR390202_1.fastq.gz

For the next command, replace 'titus' with your own NetID

In [2]:
cd /mnt/titus
/mnt/titus
In [3]:
ls
ecoli.x.salm       NC_000913.faa.pnd  NC_021814.faa.pin  reads.fa
filtered.csv       NC_000913.faa.pni  NC_021814.faa.pnd  reads.hist
formatdb.log       NC_000913.faa.psd  NC_021814.faa.pni  salm.x.ecoli
metagenome.fa      NC_000913.faa.psi  NC_021814.faa.psd  salm.x.ecoli.csv
NC_000913.faa      NC_000913.faa.psq  NC_021814.faa.psi
NC_000913.faa.phr  NC_021814.faa      NC_021814.faa.psq
NC_000913.faa.pin  NC_021814.faa.phr  ortho.csv
In [4]:
import csv
r = csv.reader(open('salm.x.ecoli.csv', 'r'))
In [5]:
scores = []

for row in r:
    name1, descr1, name2, descr2, bitscore, evalue = row
    bitscore = float(bitscore)
    scores.append(bitscore)
In [6]:
print bitscore
99.0
In [7]:
print name1, descr1, name2, descr2
ref|YP_008257983.1| hypothetical protein CFSAN001921_23440 [Salmonella enterica subsp. enterica serovar Typhimurium var. 5- str. CFSAN001921] ref|NP_415918.1| putative hexapeptide repeat acetyltransferase [Escherichia coli str. K-12 substr. MG1655]
In [8]:
hist(scores)
Out[8]:
(array([8540, 1378,  642,  227,  101,   56,   16,    8,    8,    3]),
 array([   64.7 ,   350.93,   637.16,   923.39,  1209.62,  1495.85,
        1782.08,  2068.31,  2354.54,  2640.77,  2927.  ]),
 <a list of 10 Patch objects>)
In [8]: