User: jrj.healey
jrj.healey • 2.3k
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PhD Student at the Molecular Organisation and Assembly in Cells Doctoral Training Centre, University of Warwick.
PhD is lab based primarily, utilising synthetic biology for drug delivery applications, but something of an amateur enthusiast when it comes to bioinformatics/programming. Trying to absorb as much as I can.
Decent amount of experience with molecular simulation, genomics (including assembly, QC, annotation, comparative genomics), transcriptomics, proteomics, phylogenetics etc.
Posts by jrj.healey
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... You could try using something like D3 which has python implementations to make interactive graphs etc. Here's an [online guide][1].
A friend of mine wrote BRIG in java, and then a fan of the software who wanted interactive outputs reimplemented it via D3.
[1]: http://adilmoujahid.com/posts/2015 ...
written 5 hours ago by
jrj.healey • 2.3k
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Comment:
C: Need help reading FASTQ file
... You're better off keeping the OP's `with open()` construct, as it handles file opening and closing. Your current code leaves a dangling file open. ...
written 17 hours ago by
jrj.healey • 2.3k
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Comment:
C: Need help reading FASTQ file
... If it's pointing to the line before the last line, is your input filename/path correct?
You code runs for me, though the output only returns `[+], [+], [+]` - so some of your `.readline()` logic is off too. ...
written 20 hours ago by
jrj.healey • 2.3k
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... As others have mentioned this is answered a lot on the forum. But I can't help myself when it comes to trying to make `bash` do this sort of thing.
#!/bin/bash
i=1;
while read line ; do
if [ ${line:0:1} == ">" ] ; then
echo "$line" >> seq"${i}".fasta
el ...
written 21 hours ago by
jrj.healey • 2.3k
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Comment:
C: RNA strucuture prediction
... Are you transcribing the sequence yourself first? There are loads of RNA structure predictors, but I've never seen a really thorough comparison between all of them, and a lot of the predictions are anyone's guess really.
How do you know the structure isn't predicted properly if you don't know where ...
written 22 hours ago by
jrj.healey • 2.3k
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... Close, but you're missing the transliteration from space to underscore the OP wants ;) ...
written 4 days ago by
jrj.healey • 2.3k
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... Can you provide more of your input file? You've asked that the field delimited by `|` symbols be returned, based on the accession it's paired with in the fasta header as far as we can work out - correct?
If you aren't getting the results you expect, it's likely you fasta headers aren't all in exact ...
written 4 days ago by
jrj.healey • 2.3k
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... Brain isn't functioning well enough to make one regex out of this, but it's basically just 2 string removals, and a transliteration (whitespace to underscore
$ echo "gi|556503834|ref|NC_000913.3|Escherichia coli str. K-12 substr. MG1655, complete genome" | sed -e 's/.*|//' -e 's/,.*//' | tr ' ' ...
written 5 days ago by
jrj.healey • 2.3k
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... I realise you've already got an answer, but if you want a more 'fully fledged' alternative, this is my day-to-day general purpose fasta retrieval script:
You can look for a fasta by a keyword within it's header, and it'll pull out the sequences. You can pass in a list or a string as the search quer ...
written 5 days ago by
jrj.healey • 2.3k
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129
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... If you aren't wedded to MAF format, you can get FASTA alignments of large sequences from `Kalign`, and you may well find more tools to give you back 'slices' of sequence with a fasta than with MAF - I know I've struggled with MAF in the past. ...
written 6 days ago by
jrj.healey • 2.3k
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