对于长期问题道歉，我一直在努力解决这个问题，但我无法弄清楚我做错了什么！我已经包含了一个数据示例，因此您可以看到我正在使用的内容。
我有BLAST搜索的数据输出如下：
# BLASTN 2.2.29+
# Query: Cryptocephalus androgyne
# Database: SANfive
# Fields: query id subject id % identity alignment length mismatches gap opens q. start q. end s. start s. end evalue bit score
# 7 hits found
Cryptocephalus M00964:19:000000000-A4YV1:1:2110:23842:21326 99.6 250 1 0 125 374 250 1 1.00E-128 457
Cryptocephalus M00964:19:000000000-A4YV1:1:1112:19704:18005 85.37 246 36 0 90 335 246 1 4.00E-68 255
Cryptocephalus M00964:19:000000000-A4YV1:1:2106:14369:15227 77.42 248 50 3 200 444 245 1 3.00E-34 143
Cryptocephalus M00964:19:000000000-A4YV1:1:2102:5533:11928 78.1 137 30 0 3 139 114 250 2.00E-17 87.9
Cryptocephalus M00964:19:000000000-A4YV1:1:1110:28729:12868 81.55 103 19 0 38 140 104 2 6.00E-17 86.1
Cryptocephalus M00964:19:000000000-A4YV1:1:1113:11427:16440 78.74 127 27 0 3 129 124 250 6.00E-17 86.1
Cryptocephalus M00964:19:000000000-A4YV1:1:2110:12170:20594 78.26 115 25 0 3 117 102 216 1.00E-13 75
# BLASTN 2.2.29+
# Query: Cryptocephalus aureolus
# Database: SANfive
# Fields: query id subject id % identity alignment length mismatches gap opens q. start q. end s. start s. end evalue bit score
# 10 hits found
Cryptocephalus M00964:19:000000000-A4YV1:1:2111:20990:19930 97.2 250 7 0 119 368 250 1 1.00E-118 424
Cryptocephalus M00964:19:000000000-A4YV1:1:1105:20676:23942 86.89 206 27 0 5 210 209 4 7.00E-61 231
Cryptocephalus M00964:19:000000000-A4YV1:1:1113:6534:23125 97.74 133 3 0 1 133 133 1 3.00E-60 230
Cryptocephalus M00964:21:000000000-A4WJV:1:2104:11955:19015 89.58 144 15 0 512 655 1 144 2.00E-46 183
Cryptocephalus M00964:21:000000000-A4WJV:1:1109:14814:10240 88.28 128 15 0 83 210 11 138 2.00E-37 154
Cryptocephalus M00964:21:000000000-A4WJV:1:1105:4530:13833 79.81 208 42 0 3 210 211 4 6.00E-37 152
Cryptocephalus M00964:19:000000000-A4YV1:1:2108:13133:14967 98.7 77 1 0 1 77 77 1 2.00E-32 137
Cryptocephalus M00964:19:000000000-A4YV1:1:1109:14328:3682 100 60 0 0 596 655 251 192 1.00E-24 111
Cryptocephalus M00964:19:000000000-A4YV1:1:1105:19070:25181 100 53 0 0 1 53 53 1 8.00E-21 99
Cryptocephalus M00964:19:000000000-A4YV1:1:1109:20848:27419 100 28 0 0 1 28 28 1 6.00E-07 52.8
# BLASTN 2.2.29+
# Query: Cryptocephalus cynarae
# Database: SANfive
# Fields: query id subject id % identity alignment length mismatches gap opens q. start q. end s. start s. end evalue bit score
# 2 hits found
Cryptocephalus M00964:21:000000000-A4WJV:1:2107:12228:15885 90.86 175 16 0 418 592 4 178 5.00E-62 235
Cryptocephalus M00964:21:000000000-A4WJV:1:1110:20463:5044 84.52 168 26 0 110 277 191 24 2.00E-41 167
我将此保存为csv，再次显示在下面
# BLASTN 2.2.29+,,,,,,,,,,,
# Query: Cryptocephalus androgyne,,,,,,,,,,,
# Database: SANfive,,,,,,,,,,,
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 7 hits found,,,,,,,,,,,
Cryptocephalus,M00964:19:000000000-A4YV1:1:2110:23842:21326,99.6,250,1,0,125,374,250,1,1.00E-128,457
Cryptocephalus,M00964:19:000000000-A4YV1:1:1112:19704:18005,85.37,246,36,0,90,335,246,1,4.00E-68,255
Cryptocephalus,M00964:19:000000000-A4YV1:1:2106:14369:15227,77.42,248,50,3,200,444,245,1,3.00E-34,143
Cryptocephalus,M00964:19:000000000-A4YV1:1:2102:5533:11928,78.1,137,30,0,3,139,114,250,2.00E-17,87.9
Cryptocephalus,M00964:19:000000000-A4YV1:1:1110:28729:12868,81.55,103,19,0,38,140,104,2,6.00E-17,86.1
Cryptocephalus,M00964:19:000000000-A4YV1:1:1113:11427:16440,78.74,127,27,0,3,129,124,250,6.00E-17,86.1
Cryptocephalus,M00964:19:000000000-A4YV1:1:2110:12170:20594,78.26,115,25,0,3,117,102,216,1.00E-13,75
# BLASTN 2.2.29+,,,,,,,,,,,
# Query: Cryptocephalus aureolus,,,,,,,,,,,
# Database: SANfive,,,,,,,,,,,
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 10 hits found,,,,,,,,,,,
Cryptocephalus,M00964:19:000000000-A4YV1:1:2111:20990:19930,97.2,250,7,0,119,368,250,1,1.00E-118,424
Cryptocephalus,M00964:19:000000000-A4YV1:1:1105:20676:23942,86.89,206,27,0,5,210,209,4,7.00E-61,231
Cryptocephalus,M00964:19:000000000-A4YV1:1:1113:6534:23125,97.74,133,3,0,1,133,133,1,3.00E-60,230
Cryptocephalus,M00964:21:000000000-A4WJV:1:2104:11955:19015,89.58,144,15,0,512,655,1,144,2.00E-46,183
Cryptocephalus,M00964:21:000000000-A4WJV:1:1109:14814:10240,88.28,128,15,0,83,210,11,138,2.00E-37,154
Cryptocephalus,M00964:21:000000000-A4WJV:1:1105:4530:13833,79.81,208,42,0,3,210,211,4,6.00E-37,152
Cryptocephalus,M00964:19:000000000-A4YV1:1:2108:13133:14967,98.7,77,1,0,1,77,77,1,2.00E-32,137
Cryptocephalus,M00964:19:000000000-A4YV1:1:1109:14328:3682,100,60,0,0,596,655,251,192,1.00E-24,111
Cryptocephalus,M00964:19:000000000-A4YV1:1:1105:19070:25181,100,53,0,0,1,53,53,1,8.00E-21,99
Cryptocephalus,M00964:19:000000000-A4YV1:1:1109:20848:27419,100,28,0,0,1,28,28,1,6.00E-07,52.8
我设计了一个通过百分比标识的短脚本，如果它高于阈值，则找到queryID并将其添加到列表中，然后从列表中删除重复项。
import csv
from pylab import plot,show
#Making a function to see if a string is a number or not
def is_number(s):
try:
float(s)
return True
except ValueError:
return False
#Importing the CSV file, using sniffer to check the delimiters used
#In the first 1024 bytes
ImportFile = raw_input("What is the name of your import file? ")
csvfile = open(ImportFile, "rU")
dialect = csv.Sniffer().sniff(csvfile.read(1024))
csvfile.seek(0)
reader = csv.reader(csvfile, dialect)
#Finding species over 98%
Species98 = []
Species95to97 = []
Species90to94 = []
Species85to89 = []
Species80to84 = []
Species75to79 = []
SpeciesBelow74 = []
for line in reader:
if is_number(line[2])== True:
if float(line[2])>=98:
Species98.append(line[0])
elif 97>=float(line[2])>=95:
Species95to97.append(line[0])
elif 94>=float(line[2])>=90:
Species90to94.append(line[0])
elif 89>=float(line[2])>=85:
Species85to89.append(line[0])
elif 84>=float(line[2])>=80:
Species80to84.append(line[0])
elif 79>=float(line[2])>=75:
Species75to79.append(line[0])
elif float(line[2])<=74:
SpeciesBelow74.append(line[0])
def f7(seq):
seen = set()
seen_add = seen.add
return [ x for x in seq if x not in seen and not seen_add(x)]
Species98=f7(Species98)
print len(Species98), "species over 98"
Species95to97=f7(Species95to97) #removing duplicates
search_set = set().union(Species98)
Species95to97 = [x for x in Species95to97 if x not in search_set]
print len(Species95to97), "species between 95-97"
Species90to94=f7(Species90to94)
search_set = set().union(Species98, Species95to97)
Species90to94 = [x for x in Species90to94 if x not in search_set]
print len(Species90to94), "species between 90-94"
Species85to89=f7(Species85to89)
search_set = set().union(Species98, Species95to97, Species90to94)
Species85to89 = [x for x in Species85to89 if x not in search_set]
print len(Species85to89), "species between 85-89"
Species80to84=f7(Species80to84)
search_set = set().union(Species98, Species95to97, Species90to94, Species85to89)
Species80to84 = [x for x in Species80to84 if x not in search_set]
print len(Species80to84), "species between 80-84"
Species75to79=f7(Species75to79)
search_set = set().union(Species98, Species95to97, Species90to94, Species85to89,Species80to84)
Species75to79 = [x for x in Species75to79 if x not in search_set]
print len(Species75to79), "species between 75-79"
SpeciesBelow74=f7(SpeciesBelow74)
search_set = set().union(Species98, Species95to97, Species90to94, Species85to89,Species80to84, Species75to79)
SpeciesBelow74 = [x for x in SpeciesBelow74 if x not in search_set]
print len(SpeciesBelow74), "species below 74"
#Finding species 95-97%
该脚本大部分时间都能正常运行，但每次都会出现以下错误
File "FindingSpeciesRepresentation.py", line 35, in <module>
if is_number(line[2])== "True":
IndexError: list index out of range
但是如果我更改脚本以便打印line[2]它会打印出我所期望的所有身份。你知道会出现什么问题吗？再次为数据墙道歉。
这部分来自我之前的问题：Extracting BLAST output columns in CSV form with python