我想解析一個大文本文件,這個文件在換行符中用一個字符'//'分割。我的輸入文件是這樣的:在這個腳本中的Python正則表達式實現
ID HRPA_ECOLI Reviewed; 130 AA.
AC P43329; P76861; P76863; P77479;
DE RecName: Full=ATP-dependent RNA helicase HrpA;
DE EC=3.6.4.13;
GN Name=hrpA; OrderedLocusNames=b1413, JW5905;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
DR RefSeq; NP_415931.4; NC_000913.3.
DR RefSeq; WP_000139543.1; NZ_LN832404.1.
DR ProteinModelPortal; P43329; -.
DR KEGG; ecj:JW5905; -.
DR KEGG; eco:b1413; -.
DR PATRIC; 32118112; VBIEscCol129921_1476.
DR KO; K03578; -.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.300; -; 2.
DR InterPro; IPR003593; AAA+_ATPase.
DR InterPro; IPR011545; DEAD/DEAH_box_helicase_dom.
DR InterPro; IPR011709; DUF1605.
DR Pfam; PF00270; DEAD; 1.
DR Pfam; PF11898; DUF3418; 1.
DR SMART; SM00382; AAA; 1.
DR SMART; SM00487; DEXDc; 1.
DR SMART; SM00847; HA2; 1.
DR SMART; SM00490; HELICc; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR01967; DEAH_box_HrpA; 1.
DR PROSITE; PS51192; HELICASE_ATP_BIND_1; 1.
DR PROSITE; PS51194; HELICASE_CTER; 1.
PE 3: Inferred from homology;
KW ATP-binding; Complete proteome; Helicase; Hydrolase;
KW Nucleotide-binding; Reference proteome.
FT CHAIN 1 1300 ATP-dependent RNA helicase HrpA.
FT /FTId=PRO_0000055178.
FT DOMAIN 87 250 Helicase ATP-binding.
FT {ECO:0000255|PROSITE-ProRule:PRU00541}.
FT DOMAIN 274 444 Helicase C-terminal.
SQ SEQUENCE 1300 AA; 149028 MW; A26601266D771638 CRC64;
MTEQQKLTFT ALQQRLDSLM LRDRLRFSRR LHGVKKVKNP DAQQAIFQEM AKEIDQAAGK
VLLREAARPE ITYPDNLPVS QKKQDILEAI RDHQVVIVAG ETGSGKTTQL PKICMELGRG
IKGLIGHTQP
//
ID T1RK_ECOLI Reviewed; 1170 AA.
AC P08956; Q2M5W6;
DT 01-NOV-1988, integrated into UniProtKB/Swiss-Prot.
DT 24-NOV-2009, sequence version 3.
我也有一個id.txt文件,其中的每一行都有一個唯一的ID,如:
NP_415931.4
...
我要與輸入文件中的每個ID匹配,並且如果匹配,我想用正則表達式(使用輸入文件的特定段)提取某些信息並將它們保存在輸出csv文件中。例如,對於一個匹配字符 「GO:[0-9]」,我想出了:
#!/usr/bin/env python
import re
import pdb
def peon(DATA, LIST, OUTPUT, sentinel = '\n//', pattern = re.compile('GO:[0-9]+')):
data = DATA.read()
for item in LIST:
find_me = item.strip()
j = 0
while True:
i = data.find(find_me, j)
if i < 0:
break
j = data.find(sentinel, i)
if j < 0:
j = len(data)
result = pattern.findall(data[i:j])
OUTPUT.write('{}\t{}\n'.format(find_me, ', '.join(result)))
def main(dataname, listname, outputname):
with open(dataname, 'rt') as DATA:
with open(listname, 'rt') as LIST:
with open(outputname, 'wt') as OUTPUT:
peon(DATA, LIST, OUTPUT)
if __name__ == '__main__':
main('./input_file.txt', './id.txt', './output.csv')
,這讓我像輸出:
NP_415931.4 GO:0005737, GO:0005524
現在,這是我想要的字符匹配是(編號<>標題<>描述),
1 RefSeq_ID As given in id.txt file
2 AA_Length In the line that starts with "ID" & ends with "AA."
3 Protein_Name After "RecName: Full="
4 EC_Number After "EC="
5 Organism In the line that starts with "OS"
6 NCBI_Taxid_ID After "NCBI_TaxID="
7 KEGG_ID After "KEGG;"
8 KO_ID After "KO;"
9 GO_ID As ''GO:[NUMBER]"
10 InterPro_ID After "InterPro;"
11 InterPro_Description After InterPro_ID , i.e, after 10
12 Pfam_ID After "Pfam;"
13 Pfam_Description After Pfam_ID, i.e, after 12
14 PROSITE_ID After "PROSITE;"
15 PROSITE_Description After PROSITE_ID, i.e, after 14
我還附上一個PIC更好澄清:
我想同時提取所有這些字符並將它們保存在帶有特定標題的輸出csv文件中。我改變正則表達式等之後提取,例如,「AA_Length」:
pattern = re.compile('[0-9]+ AA.')
,它給:
NP_415931.4 130 AA;
但它不完全是我所需要的模式。另外,我不確定前後匹配的正則表達式以及如何在單個腳本中實現它們。
如何在單個腳本中搜索所有這些模式並將輸出(帶標題)保存在csv文件中?
謝謝
PS:我想最終輸出的csv要看起來像:
我的excel表是在這裏:https://sites.google.com/site/iicbbioinformatics/share
從列表中的每個數據的相同位置設置的ID? –
號碼.id可以是隨機的 –