User: Frédéric Mahé

gravatar for Frédéric Mahé
Reputation:
2,930
Status:
Trusted
Location:
France, Montpellier, CIRAD
Website:
http://mahé.org/
Scholar ID:
Google Scholar Page
Last seen:
7 months, 1 week ago
Joined:
9 years, 4 months ago
Email:
f************@cirad.fr

Post-doc at the University of Kaiserslautern, Germany. Interested in bioinformatics, R, python programming and marine biology.

Posts by Frédéric Mahé

<prev • 102 results • page 1 of 11 • next >
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Answer: A: Fred's metabarcoding pipeline : Build the OTU table / keyerror in python script
... Hi, the regular expression that is used to parse [swarm][1]'s output needed to be updated to reflect the fact that [vsearch][2] does not write a ";" at the end of fasta header lines anymore (">foo;size=123;" is now ">foo;size=123"). The python script at https://github.com/frederic-mahe/swarm ...
written 12 months ago by Frédéric Mahé2.9k
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Comment: C: Splitting A Fasta File
... Hi cicindel, awk is trying to open a file descriptor for each fasta entry, and you are reaching the maximum number of files that can be opened simultaneously. To avoid that, you just need to close a file as soon as you are done with it. Here is what you need to know about awk's `close()` command: ...
written 20 months ago by Frédéric Mahé2.9k
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Answer: C: fasta files: keep only lines containing certain characters + the respective sequ
... Please [Pierre Lindenbaum][1], don't underestimate sed :-) sed -n '/^>.*18S/,/^>/ {/^>.*18S/p ; /^>/! p}' input.fa [1]: https://www.biostars.org/u/30/ ...
written 2.1 years ago by Frédéric Mahé2.9k
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Answer: A: Similarity between two sets of paired-end fastq files
... Maybe you could try [commet][1]? It was designed for metagenomics, but it allows you to compute a distance between two fastq files. [1]: https://colibread.inria.fr/software/commet/ ...
written 3.4 years ago by Frédéric Mahé2.9k
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Comment: C: BioPython: convert fasta to fastq without quality score input file
... Oops, you are right h.mom, I used the wrong symbols (`>` and `@` instead of `@` and `+`). ...
written 3.9 years ago by Frédéric Mahé2.9k
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Comment: C: python script for deleting basepair in fasta format
... Hi, the thread How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File might answer your question. ...
written 4.0 years ago by Frédéric Mahé2.9k
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Comment: C: sequence extraction from multifast file using IDs in another text file
... Yes, you can use --no-group-separator to remove these extra lines. Contrary to what is mention in the thread http://stackoverflow.com/questions/2168065/how-do-i-get-rid-of-line-separator-when-using-grep-with-context-lines, this is not an undocumented option. It is not described in man grep, but it i ...
written 4.1 years ago by Frédéric Mahé2.9k
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Comment: C: Parsing Ncbi Taxonomic Tree?
... Hello, I've just tried the scripts and they work correctly (besides a change in NCBI's FTP URL: I updated the companion script). It seems that you are using protein GIs as queries. You need to replace gi_taxid_nucl.dmp  with gi_taxid_prot.dmp. ...
written 4.1 years ago by Frédéric Mahé2.9k
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Comment: C: Best bioinfo one-liners?
... @Pierre: hum, it works well on my config (GNU Awk 4.1.1). Maybe a problem with older Awk versions (Awk < 4.0)? ...
written 4.3 years ago by Frédéric Mahé2.9k
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Comment: C: Best bioinfo one-liners?
... Even shorter! :) awk 'NR==1 {print ; next} {printf (/^>/) ? "\n"$0"\n" : $1}' file.fas ...
written 4.3 years ago by Frédéric Mahé2.9k

Latest awards to Frédéric Mahé

Student 13 months ago, asked a question with at least 3 up-votes. For How To Interpret The Scale On A Phylogenetic Tree?
Centurion 20 months ago, created 100 posts.
Epic Question 24 months ago, created a question with more than 10,000 views. For How To Interpret The Scale On A Phylogenetic Tree?
Scholar 2.1 years ago, created an answer that has been accepted. For A: How To Add Specific Word To First word in Fasta header
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: How To Add Specific Word To First word in Fasta header
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: How To Add Specific Word To First word in Fasta header
Scholar 2.6 years ago, created an answer that has been accepted. For A: How To Add Specific Word To First word in Fasta header
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Good Answer 3.2 years ago, created an answer that was upvoted at least 5 times. For A: Extraction Of Header Of Sequences In Fasta File
Commentator 3.4 years ago, created a comment with at least 3 up-votes. For C: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Good Answer 3.4 years ago, created an answer that was upvoted at least 5 times. For A: Extraction Of Header Of Sequences In Fasta File
Scholar 3.4 years ago, created an answer that has been accepted. For A: How To Add Specific Word To First word in Fasta header
Great Question 3.5 years ago, created a question with more than 5,000 views. For How To Interpret The Scale On A Phylogenetic Tree?
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Concatenating Nexus Files (For Mrbayes, Etc)
Appreciated 3.6 years ago, created a post with more than 5 votes. For A: Extraction Of Header Of Sequences In Fasta File
Appreciated 4.1 years ago, created a post with more than 5 votes. For A: Convert Non-Redundant Back To Redundant Fasta File
Commentator 4.3 years ago, created a comment with at least 3 up-votes. For C: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Scholar 4.5 years ago, created an answer that has been accepted. For A: How To Add Specific Word To First word in Fasta header
Teacher 4.5 years ago, created an answer with at least 3 up-votes. For A: Convert Non-Redundant Back To Redundant Fasta File
Good Answer 4.5 years ago, created an answer that was upvoted at least 5 times. For A: Convert Non-Redundant Back To Redundant Fasta File
Appreciated 4.5 years ago, created a post with more than 5 votes. For A: Convert Non-Redundant Back To Redundant Fasta File
Good Answer 4.6 years ago, created an answer that was upvoted at least 5 times. For A: Convert Non-Redundant Back To Redundant Fasta File
Popular Question 4.6 years ago, created a question with more than 1,000 views. For How To Interpret The Scale On A Phylogenetic Tree?
Appreciated 4.9 years ago, created a post with more than 5 votes. For A: Convert Non-Redundant Back To Redundant Fasta File
Appreciated 5.4 years ago, created a post with more than 5 votes. For A: Convert Non-Redundant Back To Redundant Fasta File

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