软件exonerate输出的结果如下，想要获得比对上的target序列
Command line: [./exonerate INPUT/UN029382.fa INPUT/scaffold125532.fa --model est2genome --showtargetgff TRUE --showvulgar no --showalignment yes --alignmentwidth 200 --bestn 1 --verbose 2]
Hostname: [node009]
C4 Alignment:
------------
Query: UN029382
Target: scaffold125532 [revcomp]
Model: est2genome
Raw score: 6062
Query range: 0 -> 1336
Target range: 23867182 -> 23861353
1 : ATCTGTTGCCCTCGCCCTTCGCAATGGCCTCCTCCTCCTCTGTCTCCCGTCCGCGGAAGCGTCCCGCCGCCGTCGCCTTTTCTTCCTCGCCTCCGCCGCCGTCGCCTTTTCTTCCTCGCCTCCGCCGCCGCCTCAG >>>> Target Intron 1 >>>> GGGCTAAGG : 145
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||++ 1301 bp ++|||||||||
23867182 : ATCTGTTGCCCTCGCCCTTCGCAATGGCCTCCTCCTCCTCTGTCTCCCGTCCGCGGAAGCGTCCCGCCGCCGTCGCCTTTTCTTCCTCGCCTCCGCCGCCGTCGCCTTTTCTTCCTCGCCTCCGCCGCCGCCTCAGgt.........................agGGGCTAAGG : 23865737
146 : ACTCTGAAATTGACACCAAAGAAGAATTTTCCCCTGATCTGGCGGACCTGTGATGTTCTTCAGCTTTATCTAAAGTCTTTTGGCAGG >>>> Target Intron 2 >>>> ACAGCTCGTTTGACGAGTCCAGAGGGACGTCAGCGAGACTACTTTGAGGCAGAGTTCT : 290
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||++ 83 bp ++||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
23865736 : ACTCTGAAATTGACACCAAAGAAGAATTTTCCCCTGATCTGGCGGACCTGTGATGTTCTTCAGCTTTATCTAAAGTCTTTTGGCAGGgt.........................agACAGCTCGTTTGACGAGTCCAGAGGGACGTCAGCGAGACTACTTTGAGGCAGAGTTCT : 23865509
291 : TTTTTAAAGAAGAAGCTGAAGATGCATTGCAGAACTGCAAAATCCCAAACATGACCATTGAATGGGCTGAAGCAAACATATCAGACAATCCACTTACAG >>>> Target Intron 3 >>>> GACCAGCACAAATTTCGTATGACCCACCAAGGTGTGACTACGATGA : 435
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||++ 74 bp ++||||||||||||||||||||||||||||||||||||||||||||||
23865508 : TTTTTAAAGAAGAAGCTGAAGATGCATTGCAGAACTGCAAAATCCCAAACATGACCATTGAATGGGCTGAAGCAAACATATCAGACAATCCACTTACAGgt.........................agGACCAGCACAAATTTCGTATGACCCACCAAGGTGTGACTACGATGA : 23865290
436 : TTTTAACATTCTGGTAAACAGCTCGAGCACAACTTTTAAATAATTCGCTTATTGGTCTGAAGCAAACATATCAGACAATCCACTTACAGGTAATGATAAGTATAAGTAAATCTTGAGCCTGCTTATTGGTTTCACGAGAAATAATTCGCTTCTGTCAATACAGGACCAGCACAA : 609
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
23865289 : TTTTAACATTCTGGTAAACAGCTCGAGCACAACTTTTAAATAATTCGCTTATTGGTCTGAAGCAAACATATCAGACAATCCACTTACAGGTAATGATAAGTATAAGTAAATCTTGAGCCTGCTTATTGGTTTCACGAGAAATAATTCGCTTCTGTCAATACAGGACCAGCACAA : 23865116
610 : ATTTCGTATGACCCACCAAGGTGTGACTACGATGATTTTAACATTCTGGTAAACAGCTCGAGCACAACTTTTAAATAATTCGCTTATTGGTCTGAA--GCA- >>>> Target Intron 4 >>>> AACATATCAGACAATC--------CACTTACAGGACCAGCAC- : 743
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| | | | | || | | | ||| ++ 525 bp ++||||| | | ||| | |||| | ||||| |
23865115 : ATTTCGTATGACCCACCAAGGTGTGACTACGATGATTTTAACATTCTGGTAAACAGCTCGAGCACAACTTTTAAATTAAGCACATGTTCCTTCGTATTGCATgt.........................agAACATGCATGCCCATCTTTGTAAGAAGTTACCTG-CCAGCTCT : 23864447
744 : -AAATTTCGTATGACCCACCAAGGTGTGACTACGATGATTT-TAACATTCTGCCATTAGTACCACAGCCACGAAACAATCCTTTTCACATAAAATGGGTATTACCTAAAATGCCGAAAAGACAACAAGGCCAGCCAGAAGAACCTCAATTACCAGCCGCTCGCTATTCCCCTGA : 914
|||| | | | || || | | || | | |||| | | | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
23864446 : TGAATTGC-TTTTTCC--TTAAAATTTAAC-ATTTTAATTTGTTTTGTGCAGCCATTAGTACCACAGCCACGAAACAATCCTTTTCACATAAAATGGGTATTACCTAAAATGCCGAAAAGACAACAAGGCCAGCCAGAAGAACCTCAATTACCAGCCGCTCGCTATTCCCCTGA : 23864277
915 : AAAAGTTAAGGTTGAGCCAGCAGACCCAAGAAAACCGGCCAAGCCGCGGTACTGGCCTAAGTTTCCAATATATCTGCCAATAAAATGACGCCTCGGATGAGAAAGGCTACATCGGCTCGCAGTAAG >>>> Target Intron 5 >>>> CTCCAGGAGTAGAAGAATC : 1059
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||++ 2501 bp ++|||||||||||||||||||
23864276 : AAAAGTTAAGGTTGAGCCAGCAGACCCAAGAAAACCGGCCAAGCCGCGGTACTGGCCTAAGTTTCCAATATATCTGCCAATAAAATGACGCCTCGGATGAGAAAGGCTACATCGGCTCGCAGTAAGgt.........................agCTCCAGGAGTAGAAGAATC : 23861631
1060 : TTTTGTTGAGAAACAAGACATTCAAGGCTCTCTTTCTCTTGTCGAGAAATAAGACATTCAAGGCTCTCTTTTCTTAAAAGAAAGTGCATTTTTTGTGGAATTGTGGGATTCGTCCCTTCACTACTTTTTTTTGGTAGAGCTGCTGTCTCCTAGAGCTTACTGTGCAATAGACAT : 1233
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
23861630 : TTTTGTTGAGAAACAAGACATTCAAGGCTCTCTTTCTCTTGTCGAGAAATAAGACATTCAAGGCTCTCTTTTCTTAAAAGAAAGTGCATTTTTTGTGGAATTGTGGGATTCGTCCCTTCACTACTTTTTTTTGGTAGAGCTGCTGTCTCCTAGAGCTTACTGTGCAATAGACAT : 23861457
1234 : GCATGAAGTATTCGTAGTCTTTTTTATTCAAGTTTAGATTTCCAAGCATATATGCTATAGCCTAAAAAAAAACTGGTCGAAATGCAGGTTTGGTCTGTTGTTG : 1336
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
23861456 : GCATGAAGTATTCGTAGTCTTTTTTATTCAAGTTTAGATTTCCAAGCATATATGCTATAGCCTAAAAAAAAACTGGTCGAAATGCAGGTTTGGTCTGTTGTTG : 23861354
# --- 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
#
scaffold125532 exonerate:est2genome gene 23861354 23867182 6062 - . gene_id 0 ; sequence UN029382 ; gene_orientation +
scaffold125532 exonerate:est2genome utr5 23867047 23867182 . - .
scaffold125532 exonerate:est2genome exon 23867047 23867182 . - . insertions 0 ; deletions 0
scaffold125532 exonerate:est2genome splice5 23867045 23867046 . - . intron_id 1 ; splice_site "GT"
scaffold125532 exonerate:est2genome intron 23865746 23867046 . - . intron_id 1
scaffold125532 exonerate:est2genome splice3 23865746 23865747 . - . intron_id 0 ; splice_site "AG"
scaffold125532 exonerate:est2genome utr5 23865650 23865745 . - .
scaffold125532 exonerate:est2genome exon 23865650 23865745 . - . insertions 0 ; deletions 0
scaffold125532 exonerate:est2genome splice5 23865648 23865649 . - . intron_id 2 ; splice_site "GT"
scaffold125532 exonerate:est2genome intron 23865567 23865649 . - . intron_id 2
scaffold125532 exonerate:est2genome splice3 23865567 23865568 . - . intron_id 1 ; splice_site "AG"
scaffold125532 exonerate:est2genome utr5 23865410 23865566 . - .
scaffold125532 exonerate:est2genome exon 23865410 23865566 . - . insertions 0 ; deletions 0
scaffold125532 exonerate:est2genome splice5 23865408 23865409 . - . intron_id 3 ; splice_site "GT"
scaffold125532 exonerate:est2genome intron 23865336 23865409 . - . intron_id 3
scaffold125532 exonerate:est2genome splice3 23865336 23865337 . - . intron_id 2 ; splice_site "AG"
scaffold125532 exonerate:est2genome utr5 23865014 23865335 . - .
scaffold125532 exonerate:est2genome exon 23865014 23865335 . - . insertions 3 ; deletions 0
scaffold125532 exonerate:est2genome splice5 23865012 23865013 . - . intron_id 4 ; splice_site "GT"
scaffold125532 exonerate:est2genome intron 23864489 23865013 . - . intron_id 4
scaffold125532 exonerate:est2genome splice3 23864489 23864490 . - . intron_id 3 ; splice_site "AG"
scaffold125532 exonerate:est2genome utr5 23864151 23864488 . - .
scaffold125532 exonerate:est2genome exon 23864151 23864488 . - . insertions 11 ; deletions 5
scaffold125532 exonerate:est2genome splice5 23864149 23864150 . - . intron_id 5 ; splice_site "GT"
scaffold125532 exonerate:est2genome intron 23861650 23864150 . - . intron_id 5
scaffold125532 exonerate:est2genome splice3 23861650 23861651 . - . intron_id 4 ; splice_site "AG"
scaffold125532 exonerate:est2genome exon 23861354 23861649 . - . insertions 0 ; deletions 0
scaffold125532 exonerate:est2genome similarity 23861354 23867182 6062 - . alignment_id 0 ; Query UN029382 ; Align 23867183 1 136 ; Align 23865746 137 96 ; Align 23865567 233 157 ; Align 23865336 390 316 ; Align 23865018 706 3 ; Align 23864489 709 16 ; Align 23864465 725 10 ; Align 23864455 736 7 ; Align 23864446 743 7 ; Align 23864439 751 7 ; Align 23864432 760 12 ; Align 23864420 773 10 ; Align 23864409 783 258 ; Align 23861650 1041 296
# --- END OF GFF DUMP ---
#
-- completed exonerate analysis
代码如下
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修改加强版代码
import re
with open('result.exonerate.txt', 'r') as f:
a =[]
for num, line in enumerate(f):
if 'Query:' in line:
b = []
d = []
print ">" + line.strip().split()[1],
elif 'Target:' in line:
print line.strip().split()[1],
elif '|' in line:
a.append(num + 1)
b.append(line.count('|'))
elif 'Query range:' in line:
print int(line.strip().split()[-1]) - int(line.strip().split()[-3]),
elif num in a:
c = re.sub(r'[^A-Z]','', line[2:-2])
d.append(c)
elif 'completed exonerate analysis' in line:
count = sum(b)
print count
print ''.join(i for i in d)版权声明：本文为msw521sg原创文章，遵循CC 4.0 BY-SA版权协议，转载请附上原文出处链接和本声明。