User: jan

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jan0
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Posts by jan

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Finding fasta files that share the highest number of identical headers
... This is a great advice. Thank you very much! I had to replace "grep -wf - *.fa" by "grep -wf *.fa". I assume the dash was added accidentally, is that right? With the dash it wasn't working. However, now it's working but for all OTUs (headers), the number of files in which they are represented is r ...
written 6 weeks ago by jan0
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Comment: C: Finding fasta files that share the highest number of identical headers
... Great, the edited version is doing the job :) Thank you, Pierre! ...
written 8 weeks ago by jan0
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Comment: C: Finding fasta files that share the highest number of identical headers
... I am getting a long list showing the number of headers, which are shared among two files each. Getting the names of the 10 files with the most shared headers remains unresolved. Anyway, thanks for trying! ...
written 8 weeks ago by jan0
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Comment: C: Finding fasta files that share the highest number of identical headers
... @Pierre and Nicolas: That's true. It gives the headers not the file names. ...
written 8 weeks ago by jan0
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Comment: C: Finding fasta files that share the highest number of identical headers
... Hi Pierre! Thanks for the fast reply. This command, however, would give me the 10 fasta files that have the highest number of redundant headers within the same file. There are no redundant headers in each of my files. What I need is to find the 10 fasta files with the highest number of identical/red ...
written 8 weeks ago by jan0
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Finding fasta files that share the highest number of identical headers
... Hello, I have about 100 fasta files and need to find those 10 that share the highest number of identical headers. I.e., I am looking for the 10 fasta files for which the number of species that are present in all of them is the highest. Any idea how to do that? A script (perl, python, bash) would be ...
perl python sequence script fasta written 8 weeks ago by jan0 • updated 8 weeks ago by 5heikki7.0k
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Comment: C: Merging of sequence chunks
... Thanks JC, the script is doing the job! ...
written 10 weeks ago by jan0
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Comment: C: Merging of sequence chunks
... Sorry, my fault. After running sudo apt install default-jdk, it worked. The tool is just great! Thank you very much :-) Could the script also be modified in a way that it accepts headers that are identical only before the "@" sign (e.g., >red@abcd and >red@efgh)? ...
written 10 weeks ago by jan0
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Comment: C: Merging of sequence chunks
... Thanks Pierre! Unfortunately, however, I don't seem to be able to install BioAlcidaejdk (there is no bioalcidaejdk.jar in dist/). Can you maybe provide some guidelines how to install this? Is it also running on a Mac? ...
written 10 weeks ago by jan0
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Merging of sequence chunks
... Hello! I would like to merge all amino acid sequences with identical names in a given fasta file (trimmed alignment). I know that this can be done for manually selected sequences with Aliview, however, I am looking for a tool or script (bash, perl, python) that allows me to do that for hundreds of ...
alignment sequence written 10 weeks ago by jan0

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