在已经剥离行后删除空格？

Question

我在从 Fasta 文件中删除所有空格时遇到问题，这是我目前使用的程序：

import re
    for line in f:
        line = line.rstrip(' \n\r')
        if line.startswith(">"):
            seqid = re.search('Segment:[(0-9)]',line).group()
            seqID.append(seqid)
        else:
            numSeq = len(line)

这是测试文件的样子（我只使用第一对只是为了显示 seqId）：

>gb:CY170782|Organism:Influenza A virus A/Santa Clara/YGA_03044/2013|Segment:1|Subtype:H3N2|Host:Human
ATTATATTCAGTATGGAAAGAATAAAAGAACTACGGAATCTGATGTCGCAGTCTCGCACTCGCGAGATAC
TGACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAGTACACATCGGGGAGACAGGAAAAGAACCC
GTCACTTAGGATGAAATGGATGATGGCAATGAAATATCCAATCACTGCTGACAAAAGGGTAACAGAAATG

>gb:CY171006|Organism:Influenza A virus A/Santa Clara/YGA_03075/2013|Segment:1|Subtype:H3N2|Host:Human
ATTATATTCAGTATGGAAAGAATAAAAGAATTACGGAATCTGATGTCGCAATCTCGCACTCGCGAGATAC
TGACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAGTACACATCGGGGAGACAGGAAAAGAACCC
GTCACTTAGGATGAAATGGATGATGGCAATGAAATACCCAATCACTGCTGACAAAAGAATAACAGAAATG

我去打印的时候，打印出来是这样的：

ATTATATTCAGTATGGAAAGAATAAAAGAACTACGGAATCTGATGTCGCAGTCTCGCACTCGCGAGATAC 70
TGACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAGTACACATCGGGGAGACAGGAAAAGAACCC 70
GTCACTTAGGATGAAATGGATGATGGCAATGAAATATCCAATCACTGCTGACAAAAGGGTAACAGAAATG 70
 0
ATTATATTCAGTATGGAAAGAATAAAAGAATTACGGAATCTGATGTCGCAATCTCGCACTCGCGAGATAC 70
TGACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAGTACACATCGGGGAGACAGGAAAAGAACCC 70
GTCACTTAGGATGAAATGGATGATGGCAATGAAATACCCAATCACTGCTGACAAAAGAATAACAGAAATG 70
 0
ATTATATTCAGTATGGAAAGAATAAAAGAACTACGGAATCTGATGTCGCAGTCTCGCACTCGCGAGATAC 70
TGACAAAAACCACAGTGGACCATATGGCCATAATTAAGAAGTACACATCGGGGAGACAGGAAAAGAACCC 70
GTCACTTAGGATGAAATGGATGATGGCAATGAAATATCCAATCACTGCTGACAAAAGGGTAACAGAAATG 70
 0

如何让它连接线并删除具有 0 个核苷酸的线？抱歉，由于睡眠不足，措辞不佳。如果您对我的问题有疑问，请随时提问。

这是完整的程序：

from __future__ import division
import re
f = open('fastatest.fasta','r')
numGC = 0;
allGC = []; #array that contains all the GC%'s
sequences = []; #The array that contains all the sequences
seqID = []; #The array that contains all seqIds
seqLen = [];
numSeq = 0
GCPercent = 0
#Concatinating the FASTA file
for line in f:
    line = line.rstrip(' \n\r')
    if line.startswith(">"):
        seqid = re.search('Segment:[(0-9)]',line).group()
        seqID.append(seqid)
    else: #Find the Length and GC%
        numSeq = len(line)
        #print seqid, numSeq
        GCPercent = (( line.count('G') + line.count('C') ) / (numSeq)*100)
        allGC.append(GCPercent);
        sequences.append(line)
        seqLen.append(numSeq)
        print "%s\t%d\t%.2f" % (seqid,numSeq,GCPercent)

我收到的输出：

Segment:1   70  40.00
Segment:1   70  44.29
Segment:1   70  38.57
Traceback (most recent call last):
  File "blah", line 20, in <module>
    GCPercent = (( line.count('G') + line.count('C') ) / (numSeq)*100)
ZeroDivisionError: division by zero

Answer 1

也许条件附加有效？

if not seqid.strip.startswith('0'):
    seqID.append(seqid)

如果没有，看看 seqid 是什么样子会有所帮助。

Answer 2

当行的长度为0时，可以直接跳到循环的下一次迭代：

numSeq = len(line)  # from your code for reference
if not numSeq:
    continue

Answer 3

鉴于文件在每个序列之后都有一个空行（也在最后一个序列之后！），这应该可行：

if line.startswith(">"):
    seqid = re.search('Segment:[(0-9)]',line).group()
    seqID.append(seqid)
    sequence = ""
elif len(line.strip()): 
    sequence += line.strip()  # three lines will make a sequence
else: #Find the Length and GC%
    numSeq = len(sequence)
    #print seqid, numSeq
    GCPercent = (( sequence.count('G') + sequence.count('C') ) / (numSeq)*100)
    allGC.append(GCPercent);
    sequences.append(sequence)
    seqLen.append(numSeq)
    print "%s\t%d\t%.2f" % (seqid,numSeq,GCPercent)

我刚刚添加了三行，并在四个位置将 line 替换为 sequence。看起来像是一个最小变化的解决方案，但我还没有测试过。

Answer 4

您可以通过检查忽略空行：

from __future__ import division
import re

numGC = 0;
allGC = []; #array that contains all the GC%'s
sequences = []; #The array that contains all the sequences
seqID = []; #The array that contains all seqIds
seqLen = [];
numSeq = 0
GCPercent = 0

with open('fastatest.fasta', 'r') as f:
    #Concatinating the FASTA file
    for line in f:
        line = line.rstrip(' \n\r')
        if line:  # non-empty line?
            if line.startswith(">"):
                seqid = re.search('Segment:[(0-9)]',line).group()
                seqID.append(seqid)
            else: #Find the Length and GC%
                numSeq = len(line)
                #print seqid, numSeq
                GCPercent = ((line.count('G') + line.count('C')) /
                             (numSeq)*100)
                allGC.append(GCPercent);
                sequences.append(line)
                seqLen.append(numSeq)
                print "%s\t%d\t%.2f" % (seqid,numSeq,GCPercent)

输出：

Segment:1   70  40.00
Segment:1   70  44.29
Segment:1   70  38.57
Segment:1   70  37.14
Segment:1   70  44.29
Segment:1   70  37.14

Answer 5

尝试使用 Biopython

from Bio import SeqIO
for record in SeqIO.parse("fasta.fas","fasta"):
     print record.id
     print record.seq

这应该删除所有新行等...

在已经剥离行后删除空格？

Removing whitespace after already stripping lines?

python

bioinformatics