<p>最后我用了一堆条件来解决这个问题。你知道吗</p>
<p>这段代码不雅观，而且涉及大量的重复，但是对于一个我将反复使用的快速而肮脏的脚本，我认为它就足够了。你知道吗</p>
<pre><code>##here, i process all the gibson primers to get the final list of primers##
##=======================================================================##
construct_num = 1
temp = []
part_num = 1
temp_row_num = 1
max_seq_num = 0
for row in gibson_primer_temp_list:
max_seq_num = 0
for x in gibson_primer_temp_list:
if int(x[1]) > construct_num:
pass
if int(x[1]) == construct_num:
max_seq_num += 1
## print('Const. number counter is at ' + str(construct_num) + ' and current maximum known number of sequences is ' + str(max_seq_num))
## print(row[1])
## if int(row[1]) < construct_num:
## while construct_num < int(row[1]):
## print(max_seq_num)
## for row in gibson_primer_temp_list:
## if int(row[1]) == construct_num:
## max_seq_num += 1
## if int(row[1]) > construct_num:
## break
#print('Construct number is ' + str(row[1]) + ' and seq. number is ' + str(row[4]))
#print('Const. number counter is ' + str(construct_num) + ' and max. seq. number is ' + str(max_seq_num) + '.')
if int(row[1]) > construct_num:
part_num = 1
while construct_num < int(row[1]):
#print('Construct number is ' + str(construct_num))
construct_num += 1
## temp_row_num += 1 #do not uncomment
#continue - not to be added back again!
if int(row[1]) == construct_num:
if int(row[4]) == max_seq_num:
#print(row)
temp.append(row)
temp_row_num += 1
#print('We are going to make primers that join the first and last part in construct ' + str(construct_num))
#print('Grabbing overhang portion from part ' + str(part_num) + ', which is sequence ' + str(row[4]) + '. It has the sequence ' + str(row[0]))
overhang = row
#print('Grabbing the first sequence...')
for x in gibson_primer_temp_list:
#print(row[1] == x[1] and x[4] == 1)
if row[1] == x[1] and x[4] == 1:
#print(x[0])
anneal = x
#print('The first sequence is ' + str(anneal))
fw_primer = overhang[0] + anneal [0]
#print('The forward primer on the first part is: ' + str(fw_primer))
primer_list.append([fw_primer, construct_num, x[2], 'fw primer'])
break
#print('Grabbing the third sequence...')
for y in gibson_primer_temp_list:
#print(row[1] == y[1] and y[4] == 3)
if row[1] == y[1] and y[4] == 3:
#print(y[0])
overhang = y
#print('The third sequence is ' + str(overhang))
break
#print('Grabbing the (n-2)th sequence...')
steps_backward = 2
target_seq_num = max_seq_num - steps_backward
for z in gibson_primer_temp_list:
#print(row[1] == z[1] and z[4] == target_seq_num)
if row[1] == z[1] and z[4] == target_seq_num:
#print(z[0])
anneal = z
#print('The n-2th sequence is ' + str(anneal))
break
re_primer = overhang[0] + anneal[0]
primer_list.append([re_primer, construct_num, z[2], 're primer'])
continue
if part_num == int(row[2]) and part_num == 1: #if the part number counter = part number
#print(row)
temp.append(row)
temp_row_num += 1
continue #do NOT delete this continue
if part_num < int(row[2]):
#print('Current part is: ' + str(part_num) + '. Upping part number.' + '\n')
part_num += 1
#do NOT add in a "continue" here
if part_num == int(row[2]) and row[3] == 'fp_anneal':
#print(row)
temp.append(row)
temp_row_num += 1
#print('Current part is: ' + str(part_num))
#print('Grabbing tp_overhang from part ' + str(part_num - 1) + '...')
x = 1
for row in temp:
x += 1
if x == temp_row_num - 1:
prev_tp_overhang = row
#print('Sequence of tp_overhang from part ' + str(part_num - 1) + ' is: ' + prev_tp_overhang[0])
fw_primer_current = prev_tp_overhang[0] + row[0]
#print('Appending to master primer list...')
primer_list.append([fw_primer_current, construct_num, part_num, 'fw primer'])
#print('Forward primer is: ' + str(fw_primer_current) + '\n')
continue
if part_num == int(row[2]) and row[3] == 'tp_anneal':
#print(row)
temp.append(row)
temp_row_num += 1
continue
if part_num == int(row[2]) and row[3] == 'fp_overhang':
#print(row)
temp.append(row)
temp_row_num += 1
#print('Current temp_row_num is ' + str(temp_row_num))
#print('Current part is: ' + str(part_num))
#print('Grabbing tp_anneal from part ' + str(part_num - 1) + '...')
x = 1
for row in temp:
x += 1
if x == temp_row_num - 5:
prev_tp_anneal = row
#print(row)
pass
#print('Sequence of tp_anneal from part ' + str(part_num - 1) + ' is: ' + prev_tp_anneal[0])
re_primer_prev = row[0] + prev_tp_anneal[0]
#print('Appending to master primer list...')
primer_list.append([re_primer_prev, construct_num, part_num - 1, 're primer'])
#print('Reverse primer for previous part is: ' + str(re_primer_prev) + '\n')
part_num += 1
continue
if part_num == int(row[2]) and row[3] == 'tp_overhang':
#print(row)
temp.append(row)
temp_row_num += 1
continue
continue
</code></pre>
<p>谢谢大家的帮助！你知道吗</p>
遍历一个列表，其中我必须从第一个项目中获取数据，以便在最后一个项目中使用
回答此问题可获得 20 贡献值，回答如果被采纳可获得 50 分。
<p>这是我之前问过的一个问题的后续问题：<a href="https://stackoverflow.com/questions/14063387/processing-a-sub-list-of-variable-size-within-a-larger-list">Processing a sub-list of variable size within a larger list</a>。你知道吗</p>
<p>我设法用itertools把一组组DNA片段取出来，但现在我面临一个不同的问题。你知道吗</p>
<p>我需要根据这些DNA片段设计引物。引物的设计包括不同DNA片段的重叠。假设我有三个DNA片段，片段a，B和C。我需要提取：</p>
<ul>
<li>C的最后20个核苷酸（n.t.）与A的前40个核苷酸（n.t.）依次连接</li>
<li>B的前20个n.t.的逆补码（RC）按顺序与A的最后一个n.t.的RC连接</li>
<li>A的最后20 n.t.与B的前40 n.t.连接</li>
<li>C的前20 n.t.的RC与B的最后40 n.t.的RC连接</li>
<li>C的最后20 n.t.与A的前40 n.t.连接</li>
<li>A的前20n.t.的RC与C的后40n.t.的RC连接</li>
</ul>
<p>我似乎无法解决这个问题，我也不知道从哪里开始这件事对我来说是最好的。。。你知道吗</p>
<p>到目前为止，我已经编写的代码只输出“group1”（有目的的，这样我就可以最小化我正在处理的视觉输出量）。在这里：</p>
<pre><code>#import BioPython Tools
from Bio.Seq import Seq
from Bio.Alphabet import IUPAC
#import csv tools
import csv
import sys
import os
import itertools
with open('constructs-to-make.csv', 'rU') as constructs:
construct_list = csv.DictReader(constructs)
def get_construct_number(row):
return row["Construct"]
def get_strategy(row):
return row["Strategy"]
## construct_list.next()
## construct_number = 1
primer_list = []
## temp_list = []
## counter = 2
groups = []
## for row in construct_list:
## print(row)
##
for key, items in itertools.groupby(construct_list, key=get_construct_number):
for subitems in items:
#here, I am trying to get the annealing portion of the Gibson sequence out
if subitems['Strategy'] == 'Gibson' and subitems['Construct'] == '1':
print(subitems['Construct'])
fw_anneal = Seq(subitems['Sequence'][0:40], IUPAC.unambiguous_dna)
print(fw_anneal)
re_anneal = Seq(subitems['Sequence'][-40:], IUPAC.unambiguous_dna).reverse_complement()
print(re_anneal)
fw_overhang = Seq(subitems['Sequence'][0:20], IUPAC.unambiguous_dna).reverse_complement()
print(fw_overhang)
re_overhang = Seq(subitems['Sequence'][-20:], IUPAC.unambiguous_dna)
print(re_overhang)
</code></pre>
<p>任何帮助都将不胜感激！你知道吗</p>
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