2.备注
3.关于程序调试
%%writefile script/cat.py
#作业1和2, cat.py
#包含了三中处理换行符的写法
import sys
def cat(file):
for line in open(file):
print line,
#------END of cat---------
def main():
if len(sys.argv) < 2: #
print >>sys.stderr, "Usage: python %s filename" % sys.argv[0] #一般提示信息输出到标准错误
sys.exit(0)
file = sys.argv[1]
cat(file)
#-------END main---------------
if __name__ == '__main__':
main()
Overwriting script/cat.py
%run script/cat data/test1.fa
>NM_001011874 gene=Xkr4 CDS=151-2091
gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcg
>NM_001195662 gene=Rp1 CDS=55-909
AGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCA
>NM_011283 gene=Rp1 CDS=128-6412
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCAC
>NM_0112835 gene=Rp15 CDS=128-6412
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCAC
%%writefile script/splitName.py
#作业3
import sys
def splitName(filename):
for line in open(filename):
if line[0] == '>':
lineL = line.split(' ')
print lineL[0]
else:
print line,
#------END splitName---------------
def main():
if len(sys.argv) < 2: #
print >>sys.stderr, "Usage: python %s filename" % sys.argv[0] #一般提示信息输出到标准错误
sys.exit(0)
filename = sys.argv[1]
splitName(filename)
#-------END main------------------
if __name__ == '__main__':
main()
Overwriting script/splitName.py
%run script/splitName data/test2.fa
>NM_001011874
gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcg
aggcgaggaggtggcgggaggaggagacagcagggacaggTGTCAGATAAAGGAGTGCTCTCCTCCGCTG
CCGAGGCATCATGGCCGCTAAGTCAGACGGGAGGCTGAAGATGAAGAAGAGCAGCGACGTGGCGTTCACC
CCGCTGCAGAACTCGGACAATTCGGGCTCTGTGCAAGGACTGGCTCCAGGCTTGCCGTCGGGGTCCGGAG
>NM_001195662
AAGCTCAGCCTTTGCTCAGATTCTCCTCTTGATGAAACAAAGGGATTTCTGCACATGCTTGAGAAATTGC
AGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCA
AGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGT
GGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGC
TGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACA
CAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTG
>NM_011283
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCAC
ACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACAC
CTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATAT
CACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGG
GTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCC
TGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGA
GGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGG
CGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATA
TGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA
>NM_0112835
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCAC
ACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACAC
CTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATAT
CACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGG
GTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCC
TGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGA
GGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGG
CGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATA
TGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA
%%writefile script/formatFasta.py
#作业4
import sys
def formatFasta(filename):
aList = []
for line in open(filename):
if line[0] == '>':
lineL = line.split(' ')
if aList:
print ''.join(aList)
aList = []
name = lineL[0]
print name
else:
aList.append(line.strip())
#不要忘了最后一个序列
print ''.join(aList)
#-----End formatFasta----------------
def main():
if len(sys.argv) < 2: #
print >>sys.stderr, "Usage: python %s filename" % sys.argv[0] #一般提示信息输出到标准错误
sys.exit(0)
filename = sys.argv[1]
formatFasta(filename)
#-------END main------------------
if __name__ == '__main__':
main()
Overwriting script/formatFasta.py
%run script/formatFasta data/test2.fa
>NM_001011874
gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcgaggcgaggaggtggcgggaggaggagacagcagggacaggTGTCAGATAAAGGAGTGCTCTCCTCCGCTGCCGAGGCATCATGGCCGCTAAGTCAGACGGGAGGCTGAAGATGAAGAAGAGCAGCGACGTGGCGTTCACCCCGCTGCAGAACTCGGACAATTCGGGCTCTGTGCAAGGACTGGCTCCAGGCTTGCCGTCGGGGTCCGGAG
>NM_001195662
AAGCTCAGCCTTTGCTCAGATTCTCCTCTTGATGAAACAAAGGGATTTCTGCACATGCTTGAGAAATTGCAGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTG
>NM_011283
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA
>NM_0112835
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA
%%writefile script/formatFasta-2.py
#作业5
import sys
def formatSeq(aList, length):
seq = ''.join(aList)
len_seq = len(seq)
for i in range(0,len_seq,length):
print seq[i:i+length]
#----END formatSeq-------------------
def formatFasta(filename,length):
aList = []
for line in open(filename):
if line[0] == '>':
lineL = line.split(' ')
if aList:
formatSeq(aList, length)
aList = []
name = lineL[0]
print name
else:
aList.append(line.strip())
#不要忘了最后一个序列
formatSeq(aList, length)
#------------END of formatFasta------------
def main():
if len(sys.argv) < 3: #注意这儿参数改变了
print >>sys.stderr, "Usage: python %s filename length_of_seq_in_each_line" % sys.argv[0] #一般提示信息输出到标准错误
sys.exit(0)
filename = sys.argv[1]
length = int(sys.argv[2])
formatFasta(filename, length)
#-------END main------------------
if __name__ == '__main__':
main()
Overwriting script/formatFasta-2.py
%run script/formatFasta-2 data/test2.fa 80
>NM_001011874
gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcgaggcgaggag
gtggcgggaggaggagacagcagggacaggTGTCAGATAAAGGAGTGCTCTCCTCCGCTGCCGAGGCATCATGGCCGCTA
AGTCAGACGGGAGGCTGAAGATGAAGAAGAGCAGCGACGTGGCGTTCACCCCGCTGCAGAACTCGGACAATTCGGGCTCT
GTGCAAGGACTGGCTCCAGGCTTGCCGTCGGGGTCCGGAG
>NM_001195662
AAGCTCAGCCTTTGCTCAGATTCTCCTCTTGATGAAACAAAGGGATTTCTGCACATGCTTGAGAAATTGCAGGTCTCACC
CAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATT
CAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTG
GTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGT
AAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCT
CCCACAATAAGAAGGTGCTG
>NM_011283
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATT
TACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATG
ATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAG
TTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTC
TGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATC
ACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAA
GGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATA
TGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA
>NM_0112835
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATT
TACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATG
ATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAG
TTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTC
TGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATC
ACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAA
GGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATA
TGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA
%%writefile script/sortFasta.py
#作业6
import sys
def readFasta(filename):
aDict = {}
for line in open(filename):
if line[0] == '>':
key = line.split()[0]
aDict[key] = [] #字典的值是一个列表, = 左边的字符串可以认为是右边列表的名字
else:
aDict[key].append(line.strip())
return aDict
#-----END readFasta-------------------
def sortFasta(aDict):
keyL = aDict.keys()
keyL.sort()
for key in keyL:
print "%s\n%s" % (key, ''.join(aDict[key]))
#--------END sortFasta--------------------
def main():
if len(sys.argv) < 2: #注意这儿参数改变了
print >>sys.stderr, "Usage: python %s filename" % sys.argv[0] #一般提示信息输出到标准错误
sys.exit(0)
filename = sys.argv[1]
aDict = readFasta(filename)
sortFasta(aDict)
#-------END main------------------
if __name__ == '__main__':
main()
Overwriting sortFasta.py
%run script/sortFasta data/test2.fa
>NM_001011874
gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcgaggcgaggaggtggcgggaggaggagacagcagggacaggTGTCAGATAAAGGAGTGCTCTCCTCCGCTGCCGAGGCATCATGGCCGCTAAGTCAGACGGGAGGCTGAAGATGAAGAAGAGCAGCGACGTGGCGTTCACCCCGCTGCAGAACTCGGACAATTCGGGCTCTGTGCAAGGACTGGCTCCAGGCTTGCCGTCGGGGTCCGGAG
>NM_001195662
AAGCTCAGCCTTTGCTCAGATTCTCCTCTTGATGAAACAAAGGGATTTCTGCACATGCTTGAGAAATTGCAGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTG
>NM_011283
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA
>NM_0112835
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA
%%writefile script/grepFasta.py
#作业7.1
import sys
def readFasta(filename):
aDict = {}
for line in open(filename):
if line[0] == '>':
key = line.split()[0][1:] #注意去掉开头的'>',只取序列的名字
aDict[key] = [] #字典的值是一个列表
else:
aDict[key].append(line.strip())
return aDict
#--------END readFasta--------------------
def main():
if len(sys.argv) < 3: #注意这儿参数改变了
print >>sys.stderr, "Usage: python %s seqFile nameFile" % sys.argv[0] #一般提示信息输出到标准错误
sys.exit(0)
seqFile = sys.argv[1]
nameFile = sys.argv[2]
aDict = readFasta(seqFile)
for line in open(nameFile):
name = line.strip()
print ">%s\n%s" % (name, ''.join(aDict[name]))
#-------END main------------------
if __name__ == '__main__':
main()
Overwriting grepFasta.py
%run script/grepFasta.py data/test2.fa data/fasta.name
>NM_001011874
gcggcggcgggcgagcgggcgctggagtaggagctggggagcggcgcggccggggaaggaagccagggcgaggcgaggaggtggcgggaggaggagacagcagggacaggTGTCAGATAAAGGAGTGCTCTCCTCCGCTGCCGAGGCATCATGGCCGCTAAGTCAGACGGGAGGCTGAAGATGAAGAAGAGCAGCGACGTGGCGTTCACCCCGCTGCAGAACTCGGACAATTCGGGCTCTGTGCAAGGACTGGCTCCAGGCTTGCCGTCGGGGTCCGGAG
>NM_011283
AATAAATCCAAAGACATTTGTTTACGTGAAACAAGCAGGTTGCATATCCAGTGACGTTTATACAGACCACACAAACTATTTACTCTTTTCTTCGTAAGGAAAGGTTCAACTTCTGGTCTCACCCAAAATGAGTGACACACCTTCTACTAGTTTCTCCATGATTCATCTGACTTCTGAAGGTCAAGTTCCTTCCCCTCGCCATTCAAATATCACTCATCCTGTAGTGGCTAAACGCATCAGTTTCTATAAGAGTGGAGACCCACAGTTTGGCGGCGTTCGGGTGGTGGTCAACCCTCGTTCCTTTAAGACTTTTGACGCTCTGCTGGACAGTTTATCCAGGAAGGTACCCCTGCCCTTTGGGGTAAGGAACATCAGCACGCCCCGTGGACGACACAGCATCACCAGGCTGGAGGAGCTAGAGGACGGCAAGTCTTATGTGTGCTCCCACAATAAGAAGGTGCTGCCAGTTGACCTGGACAAGGCCCGCAGGCGCCCTCGGCCCTGGCTGAGTAGTCGCTCCATAAGCACGCATGTGCAGCTCTGTCCTGCAACTGCCAATATGTCCACCATGGCACCTGGCATGCTCCGTGCCCCAAGGAGGCTCGTGGTCTTCCGGAATGGTGACCCGAA
%%writefile script/grepFastq.py
#作业7.2
import sys
def readFastq(seqFile):
aDict = {}
count = 0
for line in open(seqFile):
count += 1
if count % 4 == 1:
name = line.strip()[1:] #去掉开头的@
aDict[name] = [line] #存储名字行
else:
aDict[name].append(line)
#----END reading--------------
return aDict
#-------END readFastq----------这行只是注释,可有可无------
def main():
if len(sys.argv) < 3: #注意这儿参数改变了
print >>sys.stderr, "Usage: python %s seqFile nameFile" % sys.argv[0] #一般提示信息输出到标准错误
sys.exit(0)
seqFile = sys.argv[1]
nameFile = sys.argv[2]
aDict = readFastq(seqFile)
for line in open(nameFile):
name = line.strip()
print ''.join(aDict[name]),
#-------END main------------------
if __name__ == '__main__':
main()
Overwriting grepFastq.py
%run script/grepFastq data/test1.fq data/fastq.name
@HWI-ST1223:80:D1FMTACXX:2:1101:1243:2213 1:N:0:AGTCAA
TCTGTGTAGCCNTGGCTGTCCTGGAACTCACTTTGTAGACCAGGCTGGCATGCACCACCACNNNCGGCTCATTTGTCTTTNNTTTTTGTTTTGTTCTGTA
+
BCCFFFFFFHH#4AFHIJJJJJJJJJJJJJJJJJIJIJJJJJGHIJJJJJJJJJJJJJIIJ###--5ABECFFDDEEEEE##,5=@B8?CDD<AD>C:@>
@HWI-ST1223:80:D1FMTACXX:2:1101:1375:2060 1:N:0:AGTCAA
NTGCTGAGCCACGACAAGGATCCCAGAGGGCCNAGCCCTGCATCTTGTATGGACCAGTTACNCATCAAAAGAGACTACTGTAGGCACCATCAATCAGATC
+
#1:DDDD;?CFFHDFEEIGIIIIIIG;DHFGG#)0?BFBDHBFF<FCFEFD;@DD@A=7?E#,,,;=(>3;=;;C>ACCC@CCCCCBBBCCAACCCCCCC
@HWI-ST1223:80:D1FMTACXX:2:1101:1383:2091 1:N:0:AGTCAA
NGTTCGTGTGGAACCTGGCGCTAAACCATTCGTAGACGACCTGCTTCTGGGTCGGGGTTTCGTACGTAGCAGAGCAGCTCCCTCGCTGCGATCTATTGAA
+
#1=DDFDFHHHHHJGJJJJJJJJJJJJJJJIJIGDHIHIGIJJJJJJJIIIGHHFDD3>BDDBDDDDDDDDDDBDCCBDDDDDDDDDDDBBDDDDEEACD
@HWI-ST1223:80:D1FMTACXX:2:1101:1452:2138 1:N:0:AGTCAA
NTCTAGGAGGTCTAGAAAGCCCAGGCCACCGGTACAAACATCAAGGGTGTTACGGATGTGCCGCTCTGAACCTCCAGGACGACTTTGATTTCAACTACAA
+
#4=DFFEFHHHHHJJJJJIJJJJHIIJGJJJJ@GIIJJJJJJIJJJJFGHIIIJJHHHDFFFFDDDDDDDDDDDDCDDDDDDDDDDDCCCEDEDDDDDDD
%%writefile script/screenResult.py
#作业8
import sys
def screenResult(filename, fc_value, adjP_value):
head = 1 #This is used to indicate there is one head line needing to skip
for line in open(filename):
if head:
head -= 1
continue
#-----Begin data lines------
lineL = line.split()
foldChange = float(lineL[9])
adjP = float(lineL[12])
if foldChange > fc_value and adjP < adjP_value:
print lineL[0]
#-------END screenResult-------------------
def main():
if len(sys.argv) < 4: #注意这儿参数改变了
print >>sys.stderr, "Usage: python %s fileName fold_change adjP" % sys.argv[0] #一般提示信息输出到标准错误
sys.exit(0)
filename = sys.argv[1]
fc = float(sys.argv[2])
adjP = float(sys.argv[3])
screenResult(filename, fc, adjP)
#-------END main------------------
if __name__ == '__main__':
main()
Overwriting screenResult.py
%run script/screenResult data/test.expr 2 0.05
Novel00011
Novel00043
Novel00047
Novel00077
Novel00079
Novel00080
Novel00084
Novel00085
Novel00086
Novel00087
Novel00090
Novel00124
Novel00148
Novel00156
Novel00162
Novel00166
%%writefile script/transferMultipleColumToMatrix.py
#作业9
import sys
def readMultipleColFile(filename):
head = 1
tissueSet = set()
aDict = {}
for line in open(filename):
if head: #skip header line
head -= 1
continue
#-------------------------------
lineL = line.split()
gene = lineL[0]
tissue = lineL[1]
expr = lineL[2]
if gene not in aDict:
aDict[gene] = {}
assert tissue not in aDict[gene], "Duplicate tissues"
aDict[gene][tissue] = expr
tissueSet.add(tissue)
#---END reading----------------------------
tissueL = list(tissueSet)
tissueL.sort()
return tissueL, aDict
#----END readMultipleColFile--------------------------
def main():
if len(sys.argv) < 2: #注意这儿参数改变了
print >>sys.stderr, "Usage: python %s fileName" % sys.argv[0] #一般提示信息输出到标准错误
sys.exit(0)
filename = sys.argv[1]
tissueL, aDict = readMultipleColFile(filename)
print "Gene\t%s" % '\t'.join(tissueL)
for gene, tissueD in aDict.items():
exprL = [gene]
for tissue in tissueL:
exprL.append(tissueD[tissue])
print '\t'.join(exprL)
#-------END main------------------
if __name__ == '__main__':
main()
Overwriting transferMultipleColumToMatrix.py
%run script/transferMultipleColumToMatrix data/multipleColExpr.txt
Gene A-431 A-549 AN3-CA BEWO CACO-2
ENSG00000000460 25.2 14.2 10.6 24.4 14.2
ENSG00000000938 0.0 0.0 0.0 0.0 0.0
ENSG00000000457 2.8 3.4 3.8 5.8 2.9
ENSG00000000419 73.8 38.6 33.9 53.7 155.5
ENSG00000000003 21.3 32.5 38.2 31.4 63.9
ENSG00000000005 0.0 0.0 0.0 0.0 0.0
%%writefile script/reverseComplementary.py
#作业10
import sys
def reverseComplementary(string):
ATCG_dict = {'A':'T','T':'A','C':'G','G':'C', 'a':'t','t':'a','c':'g','g':'c'}
tmpL = []
for i in string:
tmpL.append(ATCG_dict[i])
tmpL.reverse()
return ''.join(tmpL)
#------END reverseComplementary-------
def main():
if len(sys.argv) < 2: #注意这儿参数改变了
print >>sys.stderr, "Usage: python %s DNAsequence" % sys.argv[0] #一般提示信息输出到标准错误
sys.exit(0)
DNA = sys.argv[1]
print reverseComplementary(DNA)
#-------END main------------------
if __name__ == '__main__':
main()
Overwriting reverseComplementary.py
%run script/reverseComplementary ACGTACGTACGTCACGTCAGCTAGAC
GTCTAGCTGACGTGACGTACGTACGT
%%writefile script/collapsemiRNAreads.py
#作业11
import sys
def collapsemiRNAreads(smRNA_file, sample, head = 1):
lineno = 0
for line in open(smRNA_file):
if head:
head -= 1
continue
#----end skip header line---
seq, value = line.split()
lineno += 1
print ">%s_%d_x%s\n%s" % (sample, lineno, value, seq)
#-------end collapsemiRNAreads------------
def main():
if len(sys.argv) < 3: #注意这儿参数改变了
print >>sys.stderr, \
"Usage: python %s smRNA_file sampleLabel (Only three letters like ESB)" % sys.argv[0] #一般提示信息输出到标准错误
sys.exit(0)
smRNA_file = sys.argv[1]
sample = sys.argv[2]
collapsemiRNAreads(smRNA_file, sample)
#-------END main------------------
if __name__ == '__main__':
main()
Overwriting collapsemiRNAreads.py
%run script/collapsemiRNAreads data/mir.collapse ESB
>ESB_1_x2
ACTGCCCTAAGTGCTCCTTCTGGC
>ESB_2_x2
ATAAGGTGCATCTAGTGCAGATA
>ESB_3_x1
TGAGGTAGTAGTTTGTGCTGTTT
>ESB_4_x1
TCCTACGAGTTGCATGGATTC
>ESB_5_x1
ACCGGGTGGAGCCGCCGCA
>ESB_6_x1
ACTGCCCTAAGTGCTCCTTCTGGT
>ESB_7_x1
TACAGGGCTGGGGATGG
>ESB_8_x1
CCCTGGATGCTGTAGGATG
>ESB_9_x1
AAAATGCTACTACTTTTGAGTC
>ESB_10_x1
TCCCTGGTGGTCTAGTGGCTAGGAT
>ESB_11_x4
CTCTTAGATCGATGTGGTGCTC
>ESB_12_x1
TTGGTGGTTCAGTGGTA
>ESB_13_x1
TCACAATTCCCCTATACCATGGGCCAT
>ESB_14_x1
CAAATGCTAGGGTTGGTGG
>ESB_15_x4
AGGCAGCTTCCACAGCA
>ESB_16_x3
GCACTGAGATGGAGTGGTGTAA
>ESB_17_x3
CTCCATTTGTTTGATGATGGA
>ESB_18_x1
GCACTGAGATGGAGTGGTGTAT
>ESB_19_x2
AGTGCCCAGAGTTTGTAGTGT
>ESB_20_x1
ATAAGGTGCATCTAGTGCTGTTAGA
>ESB_21_x9
AAAATGCTTCCACTTTGTGTG
>ESB_22_x2
GGTAATTCTAGAGCTAATACATGCCG
>ESB_23_x6
CCGGGCGGAAACACCA
>ESB_24_x1
TGAAAGGCTGACCCGCCGGGC
>ESB_25_x1
TTCGTACAGTGGTCGTAAGTTCGTGC
>ESB_26_x1
GGTTAGCACTCTGGACTC
%%writefile script/map.py
#作业12
import sys
def readRef(ref):
refD = {}
for line in open(ref):
if line[0] == '>':
name = line[1:-1]
assert name not in refD
refD[name] = []
else:
refD[name].append(line.strip())
#---------END reading----------------
for key, valueL in refD.items():
refD[key] = ''.join(valueL)
return refD
#---------END readRef----------------
def mapSeq(seq, refD):
len_seq = len(seq)
for key, value in refD.items():
pos = value.find(seq)
while pos != -1:
print "%s\t%d\t%d\t%s" % (key, pos, pos+len_seq, seq)
current = pos + 1
newpos = value[current:].find(seq)
if newpos == -1:
break
pos = current + newpos
#----------END mapSeq------------
def main():
if len(sys.argv) < 3: #注意这儿参数改变了
print >>sys.stderr, \
"Usage: python %s Ref_genome.fa reads.fa" % sys.argv[0] #一般提示信息输出到标准错误
sys.exit(0)
ref = sys.argv[1]
read = sys.argv[2]
refD = readRef(ref)
#------------------------------------
for line in open(read):
if line[0] == '>':
pass
else:
seq = line.strip()
mapSeq(seq, refD)
#-------END main------------------
if __name__ == '__main__':
main()
Overwriting map.py
%run script/map data/ref.fa data/short.fa
chr1 199 208 TGGCGTTCA
chr1 207 216 ACCCCGCTG
chr2 63 70 AAATTGC
chr3 0 7 AATAAAT
chr3 66 74 CCACACAA
chr3 206 214 ATATCACT
chr2 163 171 ATATCACT
chr3 417 423 AGAGGA
chr2 374 380 AGAGGA
chrX 137 143 AGAGGA