|
马上注册,结交更多好友,享用更多功能^_^
您需要 登录 才可以下载或查看,没有账号?立即注册
x
本帖最后由 likuo 于 2017-7-7 21:53 编辑
inputfile=open('AY810830.txt')
outputfile=open('AY810830.fasta','w')
flag=0
for line in inputfile:
if line[0:9]=='ACCESSION':
AC=line.split()[1].strip() #可以把多个命令写在一行里 先把行切割,再选取编号为1的位置(即第二个位置)并用strip删除前后的空格
outputfile.write('>'+AC+'\n') # \n为换行
elif line[0:6]=='ORIGIN':
flag=1
elif flag==1:
fields=line.split()
if fields !=[]:
seq=''.join(fields[1:])
outputfile.write(seq.upper()+'\n')
inputfile.close()
outputfile.close()
加粗部分该如何解释,下面的AY810830.txt的内容
LOCUS AY810830 705 bp mRNA linear HTC 22-JUN-2006
DEFINITION Schistosoma japonicum SJCHGC07869 protein mRNA, partial cds.
ACCESSION AY810830
VERSION AY810830.1 GI:60600350
KEYWORDS HTC.
SOURCE Schistosoma japonicum
ORGANISM Schistosoma japonicum
Eukaryota; Metazoa; Platyhelminthes; Trematoda; Digenea;
Strigeidida; Schistosomatoidea; Schistosomatidae; Schistosoma.
REFERENCE 1 (bases 1 to 705)
AUTHORS Liu,F., Lu,J., Hu,W., Wang,S.Y., Cui,S.J., Chi,M., Yan,Q.,
Wang,X.R., Song,H.D., Xu,X.N., Wang,J.J., Zhang,X.L., Zhang,X.,
Wang,Z.Q., Xue,C.L., Brindley,P.J., McManus,D.P., Yang,P.Y.,
Feng,Z., Chen,Z. and Han,Z.G.
TITLE New perspectives on host-parasite interplay by comparative
transcriptomic and proteomic analyses of Schistosoma japonicum
JOURNAL PLoS Pathog. 2 (4), E29 (2006)
PUBMED 16617374
REFERENCE 2 (bases 1 to 705)
AUTHORS Liu,F., Lu,J., Hu,W., Wang,S.-Y., Cui,S.-J., Chi,M., Yan,Q.,
Wang,X.-R., Song,H.-D., Xu,X.-N., Wang,J.-J., Zhang,X.-L.,
Wang,Z.-Q., Xue,C.-L., Brindley,P.J., McManus,D.P., Yang,P.-Y.,
Feng,Z., Chen,Z. and Han,Z.-G.
TITLE Direct Submission
JOURNAL Submitted (07-MAR-2005) Chinese National Human Genome Center at
Shanghai, 351 Guo Shoujing Road, Shanghai 201203, China
FEATURES Location/Qualifiers
source 1..705
/organism="Schistosoma japonicum"
/mol_type="mRNA"
/db_xref="taxon:6182"
/clone="SJCHGC07869"
CDS <1..545
/note="similar to insulin receptor precursor"
/codon_start=3
/product="SJCHGC07869 protein"
/protein_id="AAX26719.2"
/db_xref="GI:76155430"
/translation="HVESDKVPVASIHATLNGPGSIRITWSNPVKPNGLIIHYLLRYR
PRNHDQSYTDSNHSSSDVSLPWLTKCISMSHWSADHSEHALTSSSYIAINQKEVSRSK
RGYNANSSTTDGGISIKDLSPGSYEFQILAVSLAGNGEWSPTVIFNIPFYTDHNGTIN
RMFIELLLFTVCVPCMPHHV"
ORIGIN
1 ctcatgttga atctgataaa gttcctgtag catctattca tgcaacattg aatggtccgg
61 gaagtatccg tattacgtgg tctaatccag tcaaacctaa tggtttaatt atacattatt
121 tattgcggta tagaccaagg aatcatgatc agagttatac agatagtaac cattcgtctt
181 cagatgtgtc gctgccatgg ttgacaaaat gtatttcgat gagtcattgg tcggctgacc
241 attctgaaca cgcattgact tcaagttcat atatagctat taatcaaaaa gaagtatcac
301 gaagtaaacg tggttataat gctaatagta gtactactga tggcggaatc tcaattaaag
361 atttatcacc aggtagctat gaatttcaaa ttttagccgt ttctcttgct ggtaacggag
421 aatggagtcc aaccgtaata ttcaatattc cattctatac agaccataat ggcacaataa
481 accgtatgtt tatagaactc ttattattta cagtttgtgt cccatgtatg ccgcatcacg
541 tgtaatgttt tgattaagga gattcaaatt ttatacgttc tctcataagt gatctttact
601 tttaattgtg tgctctaaga atatacgcat tttcggttca atagattcta aaacaatgca
661 attatgagtt agatttcatt aatgcatatg taagctaatt ttcta
//
观察样本,发现一个特点:ACCESSION 的“数据”在其随后的位置,而 ORIGIN 的数据再其下方(另起一行)的位置,所以这里使用 flag 作为一次迭代的“跳板”……
|
|