seqkit grep read name partial match

[avilella]

Can seqkit grep find partial matches of the read id in a fastq.gz input file?

For example, for a fastq.gz file with read id like the one below:

@4b8af4c8-779b-45cd-9bce-7195b765bb06 runid=c4c0924f086b14c61cf8eb6b1607978c6a9990bd read=68104 ch=2069 start_time=2024-07-30T06:12:28.276857+01:00 flow_cell_id=PAW35759 protocol_group_id=LSK114-SB-B1350 sample_id=SB-B1350 parent_read_id=4b8af4c8-779b-45cd-9bce-7195b765bb06 basecall_model_version_id=dna_r10.4.1_e8.2_400bps_hac@v4.3.0

Could I have a list of read is in a file search.txt that look like the string before runid=..., e.g.:

4b8af4c8-779b-45cd-9bce-7195b765bb06

Thanks

[shenwei356]

4b8af4c8-779b-45cd-9bce-7195b765bb06 is exactly the default sequence ID, so just use the default options.

seqkit grep -f search.txt reads.fq.gz -o out.fq.gz

[avilella]

It doesn't seem to work for me: ``` $ seqkit fx2tab PAW35759_pass_83522a2c_c4c0924f_56.fastq.gz | awk '{print $1}' | head > test.txt $ head test.txt d1db3dec-0b36-4607-8828-68f14495564b 2d960d6f-7d4f-45b3-8c9f-ebb126fa6f5a c1e0188e-a560-4f56-8350-c4a9b67ca907 46fcf43b-d137-45f8-a74a-30cc12bf57d8 5e01a6fd-bb95-4bce-a65f-8f566da85cf7 d1f4bf8f-95be-4f1b-a7ca-493f2cf8909e a981d7f3-4e2f-4109-9445-1437f6a9a5a3 6d501644-5167-4e37-85c3-4bb95cb12baf 638c5e62-c0f0-4659-b4b5-8cfc6c1d41e4 bfcc4249-7e76-45f6-bc84-5124febc7b6f $ seqkit grep -f test.txt PAW35759_pass_83522a2c_c4c0924f_56.fastq.gz -o foo.fq [INFO] 10 patterns loaded from file Terminated $ cat foo.fq $ ```

[shenwei356]

It's very strange. Please provide the seqkit version,

seqkit version

and a few records of the reads file as an attached file.

seqkit head -n 10 PAW35759_pass_83522a2c_c4c0924f_56.fastq.gz -o test.fq.gz

[avilella]

seqkit v2.5.1 I am attaching 10 records

On Wed, Jul 31, 2024 at 2:35 PM Wei Shen ***@***.***> wrote: It's very strange. Please provide the seqkit version, seqkit version and a few records of the reads file as an attached file. seqkit head -n 10 PAW35759_pass_83522a2c_c4c0924f_56.fastq.gz -o test.fq.gz — Reply to this email directly, view it on GitHub <#481 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABGSNZOHGOS5OS7LRXCLOLZPDR3FAVCNFSM6AAAAABLYIRG2WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRQGU2DGMZZGA> . You are receiving this because you authored the thread.Message ID: ***@***.***>

d1db3dec-0b36-4607-8828-68f14495564b 2d960d6f-7d4f-45b3-8c9f-ebb126fa6f5a c1e0188e-a560-4f56-8350-c4a9b67ca907 46fcf43b-d137-45f8-a74a-30cc12bf57d8 5e01a6fd-bb95-4bce-a65f-8f566da85cf7 d1f4bf8f-95be-4f1b-a7ca-493f2cf8909e a981d7f3-4e2f-4109-9445-1437f6a9a5a3 6d501644-5167-4e37-85c3-4bb95cb12baf 638c5e62-c0f0-4659-b4b5-8cfc6c1d41e4 bfcc4249-7e76-45f6-bc84-5124febc7b6f

[shenwei356]

Sorry, I mean FASTQ records, not just the sequence ID.

[avilella]

test.fq.gz

I also tried with seqkit v2.8.2, same result.

[shenwei356]

I have no idea now. It woked for me.

$ seqkit seq -ni test.fq.gz -o ids.txt
$ seqkit grep -f ids.txt test.fq.gz -o out.fq.gz
$ seqkit sum --quiet test.fq.gz out.fq.gz
seqkit.v0.1_DLS_k0_4ef19986849aad9428ede02bf8ff6028     test.fq.gz
seqkit.v0.1_DLS_k0_4ef19986849aad9428ede02bf8ff6028     out.fq.gz

fx2tab and awk version

$ seqkit fx2tab test.fq.gz | awk '{print $1}' | head -n 10 > ids2.txt 
$ seqkit grep -f ids2.txt test.fq.gz -o out2.fq.gz 
[INFO] 10 patterns loaded from file

$ seqkit sum --quiet *.fq.gz
seqkit.v0.1_DLS_k0_4ef19986849aad9428ede02bf8ff6028     out2.fq.gz
seqkit.v0.1_DLS_k0_4ef19986849aad9428ede02bf8ff6028     out.fq.gz
seqkit.v0.1_DLS_k0_4ef19986849aad9428ede02bf8ff6028     test.fq.gz

Info

$ seqkit version 
seqkit v2.8.2

$ uname -a
Linux mBio 6.6.41-1-MANJARO #1 SMP PREEMPT_DYNAMIC Fri Jul 19 14:57:10 UTC 2024 x86_64 GNU/Linux

[shenwei356]

Try using cat -A to check the id files.

[avilella]

Ah! The problem seems to be with my machine LS21: Linux LS21 6.5.0-44-generic #44~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Tue Jun 18 14:36:16 UTC 2 x86_64 x86_64 x86_64 GNU/Linux If I try it on another machine with a different version of Ubuntu, it works fine.

…

On Wed, Jul 31, 2024 at 2:47 PM Wei Shen ***@***.***> wrote: Try using cat -A to check the id files. — Reply to this email directly, view it on GitHub <#481 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABGSN4SDSXDHFOCDHM5SLTZPDTIPAVCNFSM6AAAAABLYIRG2WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRQGU3DSNZVGY> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[shenwei356]

What??? How's that possible? awk's problem?
Did you try

$ seqkit seq -ni test.fq.gz -o ids.txt
$ seqkit grep -f ids.txt test.fq.gz -o out.fq.gz

[avilella]

Both commands show the Terminated stderr:

(base) petmedix@LS21:/bfx_share1/quick_share$ ~/seqkit seq -ni test.fq.gz -o ids.txt
Terminated
(base) petmedix@LS21:/bfx_share1/quick_share$ seqkit grep -f ids.txt test.fq.gz -o out.fq.gz
[WARN] 0 patterns loaded from file
Terminated

This is with a freshly downloaded version of seqkit. I wonder what could cause the binary to fail?

[shenwei356]

No idea. Forget it.