comlement fastq file using Biopython

Question

[andermachon]

HI. I try to make complement fastq file using this code:

from Bio import SeqIO
seq_=[]
with open("pass/to/input/file.fastq") as handle:
    for i in SeqIO.parse(handle,"fastq"):
        a =i.seq.complement()
        seq_.append(a)
SeqIO.write(seq_, "pass/to/output/file.fastq", "fastq")

Trying this I get error:

Traceback (most recent call last):
  File "/home/andrey/PycharmProjects/python_bio/2.py", line 7, in <module>
    SeqIO.write(seq_, "/home/andrey/genes/2.fastq", "fastq")
  File "/home/andrey/PycharmProjects/python_bio/venv/lib/python3.5/site-packages/Bio/SeqIO/__init__.py", line 497, in write
    count = writer_class(fp).write_file(sequences)
  File "/home/andrey/PycharmProjects/python_bio/venv/lib/python3.5/site-packages/Bio/SeqIO/Interfaces.py", line 215, in write_file
    count = self.write_records(records)
  File "/home/andrey/PycharmProjects/python_bio/venv/lib/python3.5/site-packages/Bio/SeqIO/Interfaces.py", line 200, in write_records
    self.write_record(record)
  File "/home/andrey/PycharmProjects/python_bio/venv/lib/python3.5/site-packages/Bio/SeqIO/QualityIO.py", line 1428, in write_record
    if record.seq is None:
AttributeError: 'Seq' object has no attribute 'seq'

In my opinion i did not add id to fastq file

hope for your help)

[finswimmer]

I was wondering whether there is a command-line-only-way to produce the reverse complement of a fastq file. And there is:

$ cat file.fastq|paste - - - -|awk -v OFS="\n" '{"echo "$2"|tr ATCG TAGC|rev"|getline seq; "echo ""\""$4"\"|rev"|getline qual; print $1, seq, $3, qual}'

BTW: Why do you want to produce a reverse complement of a fastq file?

fin swimmer

Answer 1

[andermachon]

My test fastq file:

@SEQ_ID
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
@SEQ_ID1
TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65
@SEQ_ID2
GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+
!''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65

Answer 2

[finswimmer]

Hello,

the (main) problem is this line:

a =i.seq.complement()

Try this instead:

from Bio import SeqIO


seq = open("file.fastq", "w")

with open("compl.fastq") as handle:
    for i in SeqIO.parse(handle, "fastq"):
        reverse = i.reverse_complement()

        i.seq = reverse.seq
        i.letter_annotations = reverse.letter_annotations

        SeqIO.write(i, seq, "fastq")

fin swimmer