Python学习教程 （六）

正文

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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

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