在python循环中从交替文件打印行

Question

I am trying to use python to find four-line blocks of interest in two separate files then print out some of those lines in controlled order. Below are the two input files and an example of the desired output file. Note that the DNA sequence in the Input.fasta is different than the DNA sequence in Input.fastq because the .fasta file has been read corrected.

Input.fasta

>read1
AAAGGCTGT
>read2
AGTCTTTAT
>read3
CGTGCCGCT

Input.fastq

@read1
AAATGCTGT
+
'(''%$'))
@read2
AGTCTCTAT
+
&---+2010
@read3
AGTGTCGCT
+
0-23;:677

DesiredOutput.fastq

@read1
AAAGGCTGT
+
'(''%$'))
@read2
AGTCTTTAT
+
&---+2010
@read3
CGTGCCGCT
+
0-23;:677

Basically I need the sequence line "AAAGGCTGT", "AGTCTTTAT", and "CGTGCCGCT" from "input.fasta" and all other lines from "input.fastq". This allows the restoration of quality information to a read corrected .fasta file.

Here is my closest failed attempt:

fastq = open(Input.fastq, "r")
fasta = open(Input.fasta, "r")

ReadIDs = []
IDs = []

with fastq as fq:
    for line in fq:
        if "read" in line:  
            ReadIDs.append(line)
            print(line.strip())
            for ID in ReadIDs:
                IDs.append(ID[1:6])
            with fasta as fa:
                for line in fa:
                    if any(string in line for string in IDs):
                        print(next(fa).strip())
            next(fq)
            print(next(fq).strip())
            print(next(fq).strip())

I think I am running into trouble by trying to nest "with" calls to two different files in the same loop. This prints the desired lines for read1 correctly but does not continue to iterate through the remaining lines and throws an error "ValueError: I/O operation on closed file"

Answer 1

I suggest you use Biopython , which will save you a lot of trouble as it provides nice parsers for these file formats, which handle not only the standard cases but also for example multi-line fasta.

Here is an implementation that replaces the fastq sequence lines with the corresponding fasta sequence lines:

from Bio import SeqIO

fasta_dict = {record.id: record.seq for record in
              SeqIO.parse('Input.fasta', 'fasta')}

def yield_records():
    for record in SeqIO.parse('Input.fastq', 'fastq'):
        record.seq = fasta_dict[record.id]
        yield record

SeqIO.write(yield_records(), 'DesiredOutput.fastq', 'fastq')

If you don't want to use the headers but just rely on the order then the solution is even simpler and more memory efficient (just make sure the order and number of records is the same), no need to define the dictionary first, just iterate over the records together:

fasta_records = SeqIO.parse('Input.fasta', 'fasta')
fastq_records = SeqIO.parse('Input.fastq', 'fastq')

def yield_records():
    for fasta_record, fastq_record in zip(fasta_records, fastq_records):
        fastq_record.seq = fasta_record.seq
        yield fastq_record

Answer 2

I like the Biopython solution by @Chris_Rands better for small files, but here is a solution that only uses the batteries included with Python and is memory efficient. It assumes the fasta and fastq files to contain the same number of reads in the same order.

with open('Input.fasta') as fasta, open('Input.fastq') as fastq, open('DesiredOutput.fastq', 'w') as fo:
    for i, line in enumerate(fastq):
        if i % 4 == 1:
            for j in range(2):
                line = fasta.readline()
        print(line, end='', file=fo)

Answer 3

## Open the files (and close them after the 'with' block ends)
with open("Input.fastq", "r") as fq, open("Input.fasta", "r") as fa:

    ## Read in the Input.fastq file and save its content to a list
    fastq = fq.readlines()

    ## Do the same for the Input.fasta file
    fasta = fa.readlines()


## For every line in the Input.fastq file
for i in range(len(fastq)):
    print(fastq[i]))
    print(fasta[2 * i])
    print(fasta[(2 * i) + 1])