Why does Biopython's SeqIO.parse() truncate sequences when it encounters repeated bases?
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8 weeks ago
joreamayarom ▴ 140

I'm looping through a fastq file using the method stated in this stackoverflow post.

import gzip
from Bio import SeqIO

sampleid = 'G4G3811_S77'
with gzip.open('filename.fastq.gz', 'rt') as forward_fastq:
    for forward_record in SeqIO.parse(forward_fastq, 'fastq'):
       print(sampleid + " " + forward_record.id)
       print(forward_record.seq)
       print(len(forward_record.seq))

All sequences in my fastq.gz are 151bp; however, sequences that contain repeated bases get truncated at a random (?) place before hitting the repeated segment. Is there a known explanation for this or this a bug? I checked biopython's documentation and cannot find an answer. Is there a way to get biopython not to truncate sequences? For reference, this is the output of the script provided above.

G4G3811_S77 FS10002148:5:BSB09416-2528:1:1101:13450:1010
ACAAAGCAAAAAAGCCCGCTGGAAAAGGATCCCCTTCAACTTTGCAAACCCCAGGAAGTTCTTCAGGTGCCTCTCTTCATGCTGTTGGACCTAATCAAGGTGGACTATCTCAAGGTCTTTCTGGAAAAGATTCTGCTGACAAAATGCCTTT
151
G4G3811_S77 FS10002148:5:BSB09416-2528:1:1101:9370:1040
GCGTGGTTTGGGAGGATTCTCA
22
G4G3811_S77 FS10002148:5:BSB09416-2528:1:1101:10220:1050
ACAAAGCAGAAAAGCCCGCTGGAAAAGGATCCCCTTCAACTTTGCAAACCCCAGGAAGTTCTTCAGGTGCCTCTCTTCATACTGTTGGACCTAATCAAGGTGGACTATCTCAAGGTCTTTGTGGAAAAGATTCTGCTGACTAATTGCCTTT
151
G4G3811_S77 FS10002148:5:BSB09416-2528:1:1101:10850:1050
TGTGCTTATTTCCCTTTTTTTCTTTGCC
28
G4G3811_S77 FS10002148:5:BSB09416-2528:1:1101:3240:1060
TGTGCTTATTTCCCTTTTTTTCTTTGCC
28

And this are the same sequences in the original file:

@FS10002148:5:BSB09416-2528:1:1101:13450:1010 1:N:0:77
ACAAAGCAAAAAAGCCCGCTGGAAAAGGATCCCCTTCAACTTTGCAAACCCCAGGAAGTTCTTCAGGTGCCTCTCTTCATGCTGTTGGACCTAATCAAGGTGGACTATCTCAAGGTCTTTCTGGAAAAGATTCTGCTGACAAAATGCCTTT
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@FS10002148:5:BSB09416-2528:1:1101:9370:1040 1:N:0:77
GCGTGGTTTGGGAGGATTCTCACTGTCTCTTATACACATCTCCGAGCCCACGAGACATGACAGCACATCTCGTATGCCGTCTTCTGCTTGAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+
,FF,FFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFF:FFFFFF:FFFFFF:FF,FFFFFF:,FF,F:FFFF:F,F,FFF,F:,,FFF,:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF
@FS10002148:5:BSB09416-2528:1:1101:10220:1050 1:N:0:77
ACAAAGCAGAAAAGCCCGCTGGAAAAGGATCCCCTTCAACTTTGCAAACCCCAGGAAGTTCTTCAGGTGCCTCTCTTCATACTGTTGGACCTAATCAAGGTGGACTATCTCAAGGTCTTTGTGGAAAAGATTCTGCTGACTAATTGCCTTT
+
FFF,FFFF:FFFFFF,,:F:,FF:F,,:FFFFFF,FFFFF::,:F,F,FFF,FFFF,FFFFFFFF,F,FFFFFFFF,FF:,F:,FFF,,F,,FFFFFF,FFFFFFF,FF:FF,FFF,F::,,F:FFFFFF,,FFFFF,F:,FF,:FFFF:F
@FS10002148:5:BSB09416-2528:1:1101:10850:1050 1:N:0:77
TGTGCTTATTTCCCTTTTTTTCTTTGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACATGACAGCACATCTCGTATGCCGTCTTCTGCTTGAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+
FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFF,,FFFFFFFF:FFFFFFFF,F:F,F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@FS10002148:5:BSB09416-2528:1:1101:3240:1060 1:N:0:77
TGTGCTTATTTCCCTTTTTTTCTTTGCCCTGTCTCTATACACATCTCCGAGCCCACGAGACATGACAGCACATCTGGTATGCCGTCTTCTGCTTGAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
+
:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,,F:FFFFFF:F:FFFFF:FFFF::::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
biopython • 315 views
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I cannot reproduce this issue on my laptop. I copy-pasted your FASTQ content as smpl.fq and gzipped it to smpl.fq.gz

sampleid='xyz'
with gzip.open('./smpl.fq.gz', 'rt') as fw:
     for forward_record in SeqIO.parse(fw, 'fastq'):
         print(sampleid + " " + forward_record.id)
         print(forward_record.seq)
         print(len(forward_record.seq))

xyz FS10002148:5:BSB09416-2528:1:1101:13450:1010
ACAAAGCAAAAAAGCCCGCTGGAAAAGGATCCCCTTCAACTTTGCAAACCCCAGGAAGTTCTTCAGGTGCCTCTCTTCATGCTGTTGGACCTAATCAAGGTGGACTATCTCAAGGTCTTTCTGGAAAAGATTCTGCTGACAAAATGCCTTT
151
xyz FS10002148:5:BSB09416-2528:1:1101:9370:1040
GCGTGGTTTGGGAGGATTCTCACTGTCTCTTATACACATCTCCGAGCCCACGAGACATGACAGCACATCTCGTATGCCGTCTTCTGCTTGAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
151
xyz FS10002148:5:BSB09416-2528:1:1101:10220:1050
ACAAAGCAGAAAAGCCCGCTGGAAAAGGATCCCCTTCAACTTTGCAAACCCCAGGAAGTTCTTCAGGTGCCTCTCTTCATACTGTTGGACCTAATCAAGGTGGACTATCTCAAGGTCTTTGTGGAAAAGATTCTGCTGACTAATTGCCTTT
151
xyz FS10002148:5:BSB09416-2528:1:1101:10850:1050
TGTGCTTATTTCCCTTTTTTTCTTTGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACATGACAGCACATCTCGTATGCCGTCTTCTGCTTGAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
151
xyz FS10002148:5:BSB09416-2528:1:1101:3240:1060
TGTGCTTATTTCCCTTTTTTTCTTTGCCCTGTCTCTATACACATCTCCGAGCCCACGAGACATGACAGCACATCTGGTATGCCGTCTTCTGCTTGAAAAAAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
151

I think you might be low on memory - can you try your code on the first 20000 lines of the FQ and see if that works?

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Agree with Ram - there's nothing within biopython in general that should be driving this behaviour.

Its either a hardware limitation as above, or you may need perhaps to recompile/reinstall biopython.

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