在添加先前序列的长度之后计算序列的长度(calculate the length of a sequence after adding the length of previous sequences

在添加先前序列的长度之后计算序列的长度(calculate the length of a sequence after adding the length of previous sequences)

我想确定multifasta文件中各个序列的长度。 我从生物手册中得到了这个biopython代码：

from Bio import SeqIO import sys cmdargs = str(sys.argv) for seq_record in SeqIO.parse(str(sys.argv[1]), "fasta"): output_line = '%s\t%i' % \ (seq_record.id, len(seq_record)) print(output_line)

我的输入文件如下：

>Protein1 MNT >Protein2 TSMN >Protein3 TTQRT

代码产生：

Protein1 3 Protein2 4 Protein3 5

但我想在添加先前序列的长度后计算序列的长度。 这将是：

Protein1 1-3 Protein2 4-7 Protein3 8-12

我不知道代码中的上述哪一行需要更改以获得该输出。 我对这个问题有任何帮助表示感谢，谢谢！

I want to determine length of individual sequences in a multifasta file. I got this biopython code from the bio manual as:

from Bio import SeqIO import sys cmdargs = str(sys.argv) for seq_record in SeqIO.parse(str(sys.argv[1]), "fasta"): output_line = '%s\t%i' % \ (seq_record.id, len(seq_record)) print(output_line)

My input file is like:

>Protein1 MNT >Protein2 TSMN >Protein3 TTQRT

And the code yields:

Protein1 3 Protein2 4 Protein3 5

But I want to calculate the length of a sequence after adding the length of previous sequences. It would be like:

Protein1 1-3 Protein2 4-7 Protein3 8-12

I don't know in which of the above line in the code I need to change to get that output. I'd appreciate any help on this issue, thanks!!!!

最满意答案

获得总长度很容易：

from Bio import SeqIO import sys cmdargs = str(sys.argv) total_len = 0 for seq_record in SeqIO.parse(str(sys.argv[1]), "fasta"): total_len += len(seq_record) output_line = '%s\t%i' % (seq_record.id, total_len)) print(output_line)

获得范围：

from Bio import SeqIO import sys cmdargs = str(sys.argv) total_len = 0 for seq_record in SeqIO.parse(str(sys.argv[1]), "fasta"): previous_total_len = total_len total_len += len(seq_record) output_line = '%s\t%i - %i' % (seq_record.id, previous_total_len + 1, total_len) print(output_line)

It is easy just to get the total length:

from Bio import SeqIO import sys cmdargs = str(sys.argv) total_len = 0 for seq_record in SeqIO.parse(str(sys.argv[1]), "fasta"): total_len += len(seq_record) output_line = '%s\t%i' % (seq_record.id, total_len)) print(output_line)

To get a range:

from Bio import SeqIO import sys cmdargs = str(sys.argv) total_len = 0 for seq_record in SeqIO.parse(str(sys.argv[1]), "fasta"): previous_total_len = total_len total_len += len(seq_record) output_line = '%s\t%i - %i' % (seq_record.id, previous_total_len + 1, total_len) print(output_line)