exonerate结果整理，获取target序列

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: UN029382Target: scaffold125532 [revcomp]Model: est2genomeRaw score: 6062Query range: 0 -> 1336Target range: 23867182 -> 238613531 : ATCTGTTGCCCTCGCCCTTCGCAATGGCCTCCTCCTCCTCTGTCTCCCGTCCGCGGAAGCGTCCCGCCGCCGTCGCCTTTTCTTCCTCGCCTCCGCCGCCGTCGCCTTTTCTTCCTCGCCTCCGCCGCCGCCTCAG  >>>> Target Intron 1 >>>>  GGGCTAAGG :      145||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||++         1301 bp         ++|||||||||23867182 : ATCTGTTGCCCTCGCCCTTCGCAATGGCCTCCTCCTCCTCTGTCTCCCGTCCGCGGAAGCGTCCCGCCGCCGTCGCCTTTTCTTCCTCGCCTCCGCCGCCGTCGCCTTTTCTTCCTCGCCTCCGCCGCCGCCTCAGgt.........................agGGGCTAAGG : 23865737146 : ACTCTGAAATTGACACCAAAGAAGAATTTTCCCCTGATCTGGCGGACCTGTGATGTTCTTCAGCTTTATCTAAAGTCTTTTGGCAGG  >>>> Target Intron 2 >>>>  ACAGCTCGTTTGACGAGTCCAGAGGGACGTCAGCGAGACTACTTTGAGGCAGAGTTCT :      290|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||++          83 bp          ++||||||||||||||||||||||||||||||||||||||||||||||||||||||||||23865736 : ACTCTGAAATTGACACCAAAGAAGAATTTTCCCCTGATCTGGCGGACCTGTGATGTTCTTCAGCTTTATCTAAAGTCTTTTGGCAGGgt.........................agACAGCTCGTTTGACGAGTCCAGAGGGACGTCAGCGAGACTACTTTGAGGCAGAGTTCT : 23865509291 : TTTTTAAAGAAGAAGCTGAAGATGCATTGCAGAACTGCAAAATCCCAAACATGACCATTGAATGGGCTGAAGCAAACATATCAGACAATCCACTTACAG  >>>> Target Intron 3 >>>>  GACCAGCACAAATTTCGTATGACCCACCAAGGTGTGACTACGATGA :      435|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||++          74 bp          ++||||||||||||||||||||||||||||||||||||||||||||||23865508 : TTTTTAAAGAAGAAGCTGAAGATGCATTGCAGAACTGCAAAATCCCAAACATGACCATTGAATGGGCTGAAGCAAACATATCAGACAATCCACTTACAGgt.........................agGACCAGCACAAATTTCGTATGACCCACCAAGGTGTGACTACGATGA : 23865290436 : TTTTAACATTCTGGTAAACAGCTCGAGCACAACTTTTAAATAATTCGCTTATTGGTCTGAAGCAAACATATCAGACAATCCACTTACAGGTAATGATAAGTATAAGTAAATCTTGAGCCTGCTTATTGGTTTCACGAGAAATAATTCGCTTCTGTCAATACAGGACCAGCACAA :      609||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||23865289 : TTTTAACATTCTGGTAAACAGCTCGAGCACAACTTTTAAATAATTCGCTTATTGGTCTGAAGCAAACATATCAGACAATCCACTTACAGGTAATGATAAGTATAAGTAAATCTTGAGCCTGCTTATTGGTTTCACGAGAAATAATTCGCTTCTGTCAATACAGGACCAGCACAA : 23865116610 : ATTTCGTATGACCCACCAAGGTGTGACTACGATGATTTTAACATTCTGGTAAACAGCTCGAGCACAACTTTTAAATAATTCGCTTATTGGTCTGAA--GCA-  >>>> Target Intron 4 >>>>  AACATATCAGACAATC--------CACTTACAGGACCAGCAC- :      743|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |  | | | ||  |  | |  ||| ++          525 bp         ++|||||    | | |||         | ||||  | ||||| | 23865115 : ATTTCGTATGACCCACCAAGGTGTGACTACGATGATTTTAACATTCTGGTAAACAGCTCGAGCACAACTTTTAAATTAAGCACATGTTCCTTCGTATTGCATgt.........................agAACATGCATGCCCATCTTTGTAAGAAGTTACCTG-CCAGCTCT : 23864447744 : -AAATTTCGTATGACCCACCAAGGTGTGACTACGATGATTT-TAACATTCTGCCATTAGTACCACAGCCACGAAACAATCCTTTTCACATAAAATGGGTATTACCTAAAATGCCGAAAAGACAACAAGGCCAGCCAGAAGAACCTCAATTACCAGCCGCTCGCTATTCCCCTGA :      914|||| | | |  ||    ||  | | || |   | |||| |    | | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||23864446 : TGAATTGC-TTTTTCC--TTAAAATTTAAC-ATTTTAATTTGTTTTGTGCAGCCATTAGTACCACAGCCACGAAACAATCCTTTTCACATAAAATGGGTATTACCTAAAATGCCGAAAAGACAACAAGGCCAGCCAGAAGAACCTCAATTACCAGCCGCTCGCTATTCCCCTGA : 23864277915 : AAAAGTTAAGGTTGAGCCAGCAGACCCAAGAAAACCGGCCAAGCCGCGGTACTGGCCTAAGTTTCCAATATATCTGCCAATAAAATGACGCCTCGGATGAGAAAGGCTACATCGGCTCGCAGTAAG  >>>> Target Intron 5 >>>>  CTCCAGGAGTAGAAGAATC :     1059||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||++         2501 bp         ++|||||||||||||||||||23864276 : AAAAGTTAAGGTTGAGCCAGCAGACCCAAGAAAACCGGCCAAGCCGCGGTACTGGCCTAAGTTTCCAATATATCTGCCAATAAAATGACGCCTCGGATGAGAAAGGCTACATCGGCTCGCAGTAAGgt.........................agCTCCAGGAGTAGAAGAATC : 238616311060 : TTTTGTTGAGAAACAAGACATTCAAGGCTCTCTTTCTCTTGTCGAGAAATAAGACATTCAAGGCTCTCTTTTCTTAAAAGAAAGTGCATTTTTTGTGGAATTGTGGGATTCGTCCCTTCACTACTTTTTTTTGGTAGAGCTGCTGTCTCCTAGAGCTTACTGTGCAATAGACAT :     1233||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||23861630 : TTTTGTTGAGAAACAAGACATTCAAGGCTCTCTTTCTCTTGTCGAGAAATAAGACATTCAAGGCTCTCTTTTCTTAAAAGAAAGTGCATTTTTTGTGGAATTGTGGGATTCGTCCCTTCACTACTTTTTTTTGGTAGAGCTGCTGTCTCCTAGAGCTTACTGTGCAATAGACAT : 238614571234 : 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 countprint ''.join(i for i in d)

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