编辑 ：我知道feature.type将提供基因/ CDS，然后feature.qualifiers将提供“db_xref”/“locus_tag”/“推断“等等是否有feature.对象允许我直接访问该位置（例如：[5240:7267](+)）？
此网址提供了更多信息，但我无法弄清楚如何将其用于我的目的...... http://biopython.org/DIST/docs/api/Bio.SeqFeature.SeqFeature-class.html#location_operator
原帖：
我正在尝试修改GenBank文件中功能的位置。基本上，我想修改GenBank文件的以下位：
gene 5240..7267
/db_xref="GeneID:887081"
/locus_tag="Rv0005"
/gene="gyrB"
CDS 5240..7267
/locus_tag="Rv0005"
/inference="protein motif:PROSITE:PS00177"
...........................
到
gene 5357..7267
/db_xref="GeneID:887081"
/locus_tag="Rv0005"
/gene="gyrB"
CDS 5357..7267
/locus_tag="Rv0005"
/inference="protein motif:PROSITE:PS00177"
.............................
请注意从 5240 到 5357 的更改
到目前为止，通过搜索互联网和Stackoverflow，我有：
from Bio import SeqIO
gb_file = "mtbtomod.gb"
gb_record = SeqIO.parse(open(gb_file, "r+"), "genbank")
rvnumber = 'Rv0005'
newstart = 5357
final_features = []
for record in gb_record:
for feature in record.features:
if feature.type == "gene":
if feature.qualifiers["locus_tag"][0] == rvnumber:
if feature.location.strand == 1:
feature.qualifiers["amend_position"] = "%s:%s" % (newstart, feature.location.end+1)
else:
# do the reverse for the complementary strand
final_features.append(feature)
record.features = final_features
with open("testest.gb","w") as testest:
SeqIO.write(record, testest, "genbank")
这基本上会创建一个名为“amend_position”的新限定符。但是，我想要做的是直接修改位置（无论是否创建新文件......）
Rv0005只是我需要更新的locus_tag的一个例子。我还有大约600个地点需要更新，这解释了对脚本的需求..帮助！
答案 0 :(得分：1)
好的，我有一些现在完全有效的东西。我会发布代码以防任何人需要类似的东西
__author__ = 'Kavin'
from Bio import SeqIO
from Bio import SeqFeature
import xlrd
import sys
import re
workbook = xlrd.open_workbook(sys.argv[2])
sheet = workbook.sheet_by_index(0)
data = [[sheet.cell_value(r, c) for c in range(sheet.ncols)] for r in range(sheet.nrows)]
# Create dicts to store TSS data
TSS = {}
row = {}
# For each entry (row), store the startcodon and strand information
for i in range(2, sheet.nrows - 1):
if data[i][5] < -0.7: # Ensures BASS score is within significant range
Gene = data[i][0]
row['Direction'] = str(data[i][3])
row['StartCodon'] = int(data[i][4])
TSS[str(Gene)] = row
row = {}
else:
i += 1
# Create an output filename based on input filename
outfile_init = re.search('(.*)\.(\w*)', sys.argv[1])
outfile = str(outfile_init.group(1)) + '_modified.' + str(outfile_init.group(2))
final_features = []
for record in SeqIO.parse(open(sys.argv[1], "r"), "genbank"):
for feature in record.features:
if feature.type == "gene" or feature.type == "CDS":
if TSS.has_key(feature.qualifiers["locus_tag"][0]):
newstart = TSS[feature.qualifiers["locus_tag"][0]]['StartCodon']
if feature.location.strand == 1:
feature.location = SeqFeature.FeatureLocation(SeqFeature.ExactPosition(newstart - 1),
SeqFeature.ExactPosition(
feature.location.end.position),
feature.location.strand)
else:
feature.location = SeqFeature.FeatureLocation(
SeqFeature.ExactPosition(feature.location.start.position),
SeqFeature.ExactPosition(newstart), feature.location.strand)
final_features.append(feature) # Append final features
record.features = final_features
with open(outfile, "w") as new_gb:
SeqIO.write(record, new_gb, "genbank")
这假定使用python program.py <genbankfile> <excel spreadsheet>
这也假定使用以下格式的电子表格：
基因同义词Tuberculist_annotated_start Orientation Re-annotated_start BASS_score
Rv0005 gyrB 5240 + 5357 -1.782
Rv0012 Rv0012 14089 + 14134 -1.553
Rv0018c pstP 23181 - 23172 -2.077
Rv0032 bioF2 34295 + 34307 -0.842
Rv0037c Rv0037c 41202 - 41163 -0.554
答案 1 :(得分：0)
所以，你可以试试下面的东西。因为变化的数量将等于文件中发现的CDS /基因的数量。您可以从csv / text文件中读取位置/位置，并制作一个像我手动制作的列表change_values。
import re
f = open("test.txt")
change_values=["1111", "2222"]
flag = True
next = 0
for i in f.readlines():
if i.startswith(' CDS') or i.startswith(' gene'):
out = re.sub(r"\d+", str(change_values[next]), i)
#Instead of print write
print out
flag = not flag
if flag==True:
next += 1
else:
#Instead of print write
print i
Amy sample test.txt文件如下所示：
gene 5240..7267
/db_xref="GeneID:887081"
/locus_tag="Rv0005"
/gene="gyrB"
CDS 5240..7267
/locus_tag="Rv0005"
/inference="protein motif:PROSITE:PS00177"
...........................
gene 5240..7267
/db_xref="GeneID:887081"
/locus_tag="Rv0005"
/gene="gyrB"
CDS 5240..7267
/locus_tag="Rv0005"
/inference="protein motif:PROSITE:PS00177"
...........................
希望，这将解决您的问题。干杯！
答案 2 :(得分：0)
我认为这可以使用原生biopython synthax完成，没有正则表达式 需要的，最小的工作示例：
from Bio import SeqIO
from Bio import SeqFeature
import copy
gbk = SeqIO.read('./test_gbk', 'gb')
index = 1
feature_to_change = copy.deepcopy(gbk.features[index]) #depends what feature you want to change,
#can also be done with loop if you want to change them all, or by some function...
new_start = 0
new_end = 100
new_feature_location = SeqFeature.FeatureLocation(new_start, new_end, feature.location.strand) #create a new feature location object
feature_to_change.location = new_feature_location #change old feature location
del gbk.features[index] #remove changed feature
gkb.features.append(feature_to_change) #add identical feature with new location
gbk.features = sorted(gbk.features, key = lambda feature: feature.location.start) # if you want them sorted by the start of the location, which is the usual case
SeqIO.write(gbk, './test_gbk_with_new_feature', 'gb')