输入文件格式
C4 Alignment:
------------
Query: UN074481
Target: scaffold9929 [revcomp]
Model: est2genome
Raw score: 2379
Query range: 0 -> 510
Target range: 1114739 -> 1048547
1 : CGCACACCACACAACCACTCACGCCATGGAACACACATCACACAACCACCCACCAACTAACACATCCATGGCCACGGAACGCACACCACACAGCCACCCTCCAACACATCCATGGCCGGCGCGGGCAAGCAGGCCATCCGCGGGGGCGGGGAGCAGGGCGGCCGCACTTGGCGGAT : 176
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
1114739 : CGCACACCACACAACCACTCACGCCATGGAACACACATCACACAACCACCCACCAACTAACACATCCATGGCCACGGAACGCACACCACACAGCCACCCTCCAACACATCCATGGCCGGCGCGGGCAAGCAGGCCATCCGCGGGGGCGGGGAGCAGGGCGGCCGCACTTGGCGGAT : 1114564
177 : GCACGAGCGGTGAGCAGGGCGGTGCCGCGGGCGGCGCCGCGGGCACGGAGCAGGGCCACCGCGCTGGCAGCGAGCTTGGCGGATGCTCGGGCGACGAGCTTGCCGGACGCGCGGGCGACGAGCATGGCGCGCAGCGGCGGCTCACTCCACCGTCGACTGCTCAGCGCAA >>>> : 346
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||+-
1114563 : GCACGAGCGGTGAGCAGGGCGGTGCCGCGGGCGGCGCCGCGGGCACGGAGCAGGGCCACCGCGCTGGCAGCGAGCTTGGCGGATGCTCGGGCGACGAGCTTGCCGGACGCGCGGGCGACGAGCATGGCGCGCAGCGGCGGCTCACTCCACCGTCGACTGCTCAGCGCAAgg..... : 1114392
347 : Target Intron 1 >>>> GGGCGCGACGGATTCTTCCCTCGGGCGCGCGGCAGCCTCTTCGCTCGGGCGCGCGGTGGCATCTTTCCTAGAGCATGGCGCGTGACGGCCACTACAGAGGAGCTCCTCCCTCCGGCGTCGGCCACCCGACACTGCACTGGCGCCCGGCTGTCCC : 499
65682 bp +-||||| | ||| ||||||||||||||||||||| |||||||||||||||||||||||||| |||| ||| |||||||| |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| || |||||||
1114391 : ....................aaGGGCGTGGCGGCTTCTTCCCTCGGGCGCGCGGCGGCCTCTTCGCTCGGGCGCGCGGTGGCCTCTTCCCTCGAGCATGGTGCGTGACGGCCACTACAGAGGAGCTCCTCCCTGCGGCGTCGGCCACCCGACACTGCACTGGCGCGCGACTGTCCC : 1048559
500 : CCCCCCCCCCC : 510
|| || | | |
1048558 : CCTCCTCTCTC : 1048548
# --- START OF GFF DUMP ---
#
#
##gff-version 2
##source-version exonerate:est2genome 2.2.0
##date 2016-06-22
##type DNA
#
#
# seqname source feature start end score strand frame attributes
#
scaffold9929 exonerate:est2genome gene 1048548 1114739 2379 - . gene_id 0 ; sequence UN074481 ; gene_orientation +
scaffold9929 exonerate:est2genome utr5 1114395 1114739 . - .
scaffold9929 exonerate:est2genome exon 1114395 1114739 . - . insertions 0 ; deletions 0
scaffold9929 exonerate:est2genome splice5 1114393 1114394 . - . intron_id 1 ; splice_site "GG"
scaffold9929 exonerate:est2genome intron 1048713 1114394 . - . intron_id 1
scaffold9929 exonerate:est2genome splice3 1048713 1048714 . - . intron_id 0 ; splice_site "AA"
scaffold9929 exonerate:est2genome exon 1048548 1048712 . - . insertions 0 ; deletions 0
scaffold9929 exonerate:est2genome similarity 1048548 1114739 2379 - . alignment_id 0 ; Query UN074481 ; Align 1114740 1 345 ; Align 1048713 346 165
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
Command line: [./exonerate INPUT/UN183704.fa INPUT/scaffold9929.fa --model est2genome --showtargetgff TRUE --showvulgar no --showalignment yes --alignmentwidth 200 --bestn 1 --verbose 2]
Hostname: [node009]
想要匹配竖线（|）下边的行，并保留这一行所有的大写字母
最后的结果
CGCACACCACACAACCACTCACGCCATGGAACACACATCACACAACCACCCACCAACTAACACATCCATGGCCACGGAACGCACACCACACAGCCACCCTCCAACACATCCATGGCCGGCGCGGGCAAGCAGGCCATCCGCGGGGGCGGGGAGCAGGGCGGCCGCACTTGGCGGAT
GCACGAGCGGTGAGCAGGGCGGTGCCGCGGGCGGCGCCGCGGGCACGGAGCAGGGCCACCGCGCTGGCAGCGAGCTTGGCGGATGCTCGGGCGACGAGCTTGCCGGACGCGCGGGCGACGAGCATGGCGCGCAGCGGCGGCTCACTCCACCGTCGACTGCTCAGCGCA
GGGCGTGGCGGCTTCTTCCCTCGGGCGCGCGGCGGCCTCTTCGCTCGGGCGCGCGGTGGCCTCTTCCCTCGAGCATGGTGCGTGACGGCCACTACAGAGGAGCTCCTCCCTGCGGCGTCGGCCACCCGACACTGCACTGGCGCGCGACTGTCCC
CCTCCTCTCTC
import re
with open('result.exonerate.txt', 'r') as f:
a =[]
for num, line in enumerate(f):
if '|' in line:
a.append(num + 1)
if 'Query:' in line:
print ">" + line.strip().split()[1],
elif 'Target:' in line:
print line.strip().split()[1]
elif num in a:
b = re.sub(r'[^A-Z]','', line[2:-2])
print b