User: mforthman
mforthman • 30
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Posts by mforthman
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... Running fastq-generated SRA files from NCBI through prinseq-lite. The program generates an error:
Use of uninitialized value $qual in scalar chomp at /apps/prinseq/0.20.4/bin/prinseq-lite.pl line 2583, line 26875674.
It still continues on until it has finished, but clearly there is somethin ...
written 10 months ago by
mforthman • 30
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... I have been trying to download SRA data from NCBI and putting it in fastq format using fastq-dump. A colleague and I have been trying to figure out why the resulting fastq files are causing some errors when inputted into prinseq-lite.
My collaborator has been using this fastq-dump command:
fas ...
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... I've still been tinkering with the script and feel as though I might be getting closer to the solution:
#!/usr/bin/env python
import sys
import re
original_fn = sys.argv[1]
company_fn = sys.argv[2]
pattern = '(uce.+$|ENSOFAS.+$|[AB]_[0-9]+$)'
map = {} ...
written 16 months ago by
mforthman • 30
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... You are correct, that was my mistake. Thanks for catching that! And I appreciate you taking a further look at this later. ...
written 16 months ago by
mforthman • 30
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... Correct, I kept the original question simple in original post. In reality, the company.fasta file had many differently formatted headers. I used the script you had provided to process just the `uce` headers, which worked. I already had the `ENSOFAS` headers. This leaves the others to be formatted. T ...
written 16 months ago by
mforthman • 30
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... Thanks for the info. I've modified the regex pattern to also skip over other headers that shouldn't be modified, e.g., like the ones in the original posting (they are all in one file). If I tested correctly, the new pattern is `(uce | ENSOFAS | _[AB]_[0-9]+$)`. Regarding the last part of your reply, ...
written 16 months ago by
mforthman • 30
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... How might this script be modified to deal with other headers that are formatted differently in the company.fasta file? Specifically, I'm targeting the following example headers now:
>Clavigralla_tomentosicollis_gi_512427358_gb_GAJX01007276.1_0_rc
TGAGAAGCTCTCGCAGTCACACTGGCCCACGACCACTCTCA ...
written 16 months ago by
mforthman • 30
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... I had a similar situation posted [here][1], which was resolved, but I'm now dealing with differently formatted headers. I have two DNA sequence files I'm working with. One file (e.g., 'company.fasta') has headers that I need to change based on corresponding headers from another file (e.g., 'original ...
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... PERFECT! Thank you and everyone else for all of your help. ...
written 17 months ago by
mforthman • 30
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... Example original headers from one dataset source:
>uce-2015_p10 |design:hemiptera-v1,designer:faircloth,probes-locus:uce-2015,probes-probe:10,probes-source:oncfas1,probes-global-chromo:Scaffold80,probes-global-start:539805,probes-global-end:539925,probes-local-start:40,probes-local-end:160
...
written 17 months ago by
mforthman • 30
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