Moderator: jrj.healey

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jrj.healey9.8k
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Recently finished my PhD, so now I pretend to know what I’m talking about on Bioinformatics forums...

Posts by jrj.healey

<prev • 1,783 results • page 2 of 179 • next >
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Comment: C: GenBank features don't extract sequences based on condition Biopython
... Another small comment, I assume its elsewhere in your script, but you haven't declared the vector `intergenic_sequence` in that code snippet, so as posted, it would fail based on that alone. ...
written 1 day ago by jrj.healey9.8k
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Answer: A: GenBank features don't extract sequences based on condition Biopython
... I'm not 100% sure if this code is right, but hopefully it gets you closer to the desired outcome. It's too late in the day for me to debug your code so it seemed easier to sort of start over. import sys from Bio import SeqIO entry = SeqIO.read(sys.argv[1], 'genbank') # This will ne ...
written 1 day ago by jrj.healey9.8k
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Comment: C: Running PAML without Tree file?
... Yeah, there's essentially no such thing as a genome-scale multiple alignment tool. Your approach simply isn't possible. Under other circumstances (estimating distance for instance) I'd suggest you could get by with multiple pairwise alignment, but for dNdS that isn't the case. You could select a su ...
written 1 day ago by jrj.healey9.8k
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Comment: C: Running PAML with out Tree file?
... CLUSTAL absolutely will not be able to handle full genome-scale alignments. There are few tools that really can. LASTZ is one of the few tools I've seen that deals with large sequences but even then, 18 is probably too many, and I don't know how big your genomes are (in my experience its alignments ...
written 1 day ago by jrj.healey9.8k
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Answer: C: Running PAML with out Tree file?
... You need to calculate the tree empirically because things like branch lengths may be important. It would be possible to hand-write a tree with appropriate topology, but without distances it may give you false results. Furthermore, in an ideal world, the tree you use to describe your data should be ...
written 1 day ago by jrj.healey9.8k
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Comment: C: ETE3 TreeError: 'Nodes are not connected!': how to fix?
... That is pretty weird. I’ve certainly never seen it before. Perhaps this is one to submit to their issue tracker. Could you share an example problematic tree and your versions of python/ETE etc to see if others can reproduce? ...
written 1 day ago by jrj.healey9.8k
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Comment: C: GenBank features don't extract sequences based on condition Biopython
... Can you provide a link to one of your input genbanks and I'll have a little play with the data myself. ...
written 1 day ago by jrj.healey9.8k
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Comment: C: ETE3 TreeError: 'Nodes are not connected!': how to fix?
... Is your tree file malformed in some way? ...
written 1 day ago by jrj.healey9.8k
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Comment: C: Changing file name with sed command
... Glad it helped. Be sure to accept it to provide closure to the thread if it resolved your problem. ...
written 1 day ago by jrj.healey9.8k
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Comment: C: Changing file name with sed command
... Just be a little cautious with all the `/`'s in those names. That'll look like a directory structure to bash. e.g. `touch 'H3K4me1/Cell-Line=S2-DRSC#Developmental-Stage=Late-Embryonic-stage#Tissue=Embryo-derived-cell-line/ChIP-chip/Rep-1//Dmel_r5.32/modENCODE_304.gff3'` fails miserably, even when h ...
written 1 day ago by jrj.healey9.8k

Latest awards to jrj.healey

Good Answer 16 hours ago, created an answer that was upvoted at least 5 times. For C: Exporting sequences from Excel
Scholar 1 day ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Appreciated 1 day ago, created a post with more than 5 votes. For A: install some bioinformatic sofwares without root
Scholar 1 day ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 1 day ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar 2 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 5 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Popular Question 6 days ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Scholar 8 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 8 days ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Scholar 10 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 26 days ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: install some bioinformatic sofwares without root
Scholar 5 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Popular Question 5 weeks ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Scholar 6 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Scholar 6 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Replace Sequence IDs in many text files (newick format) - Change script
Scholar 6 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: fasta seq header
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Merging gff/gbk to create a 'full' gbk
Scholar 8 weeks ago, created an answer that has been accepted. For A: Script/Application to create a genbank format sub-sequence
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: How do can I use Biopython and SeqIO to parse out multiple genes from several NC

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