User: Leonardo Normando

Reputation:
60
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Location:
Brazil
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http://w
Last seen:
4 months, 1 week ago
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7 years, 9 months ago
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Posts by Leonardo Normando

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Batch rename *fastq.gz files using regular expression
... Yeah! I saw the parameters that after running the script and was amazed to see that option (couldn't test since I already had deleted the folder XD ) Thanks also for the `seqkit` [software](https://github.com/shenwei356/seqkit), Shen Wei! ...
written 15 months ago by Leonardo Normando60
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Comment: C: Batch rename *fastq.gz files using regular expression
... When running on: python --version Python 3.6.5 :: Anaconda, Inc. I've got: File "rename_fastq.py", line 6 print file, '\t', file.split('_')[0] + '_' + file.split('_')[3] + '_.fastq.gz' ^ SyntaxError: invalid syntax But, using a Python 2.7.15 environment ...
written 15 months ago by Leonardo Normando60
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Comment: C: Batch rename *fastq.gz files using regular expression
... Hello! I want to keep the '_' after the R* just to keep my sanity while running other scripts (that check for the patter _R*_ ) I've got a syntax error while running your script: import os, glob for file in glob.glob("/*.fastq.gz"): ^ SyntaxError: invalid syn ...
written 15 months ago by Leonardo Normando60
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Comment: C: Batch rename *fastq.gz files using regular expression
... Thanks! It works as intended! Just modified to include the underscore after the _(R[0-9])_ part {and changed the range to [1-2]} rename -n 's/(\w_).*_(R[1-2]_).*(.fastq.gz)/$1$2$3/' *.fastq.gz ...
written 15 months ago by Leonardo Normando60
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Comment: C: Batch rename *fastq.gz files using regular expression
... Almost there! - The first group was including the second tag in the filename (eg. _S90_), hence the addition of the second " _.+ " - Changed the structure of the expression to include the underscore after the _R[12] The command with the final changes: brename -p '^(\w+)_.+_.+(_R[12]_).+' ...
written 15 months ago by Leonardo Normando60
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Batch rename *fastq.gz files using regular expression
... I'm trying to get a regex to work with rename; I've tried the approach of similar answered questions here but couldn't get the results I wanted. The files are named as such: SR1_S90_L001_R1_001.fastq.gz SR1_S90_L001_R2_001.fastq.gz Rinc_S96_L001_R1_001.fastq.gz Rinc_S96_L001_R2_0 ...
rename perl fastq regex written 15 months ago by Leonardo Normando60 • updated 15 months ago by cpad011212k
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Answer: A: Tools For Metagenomic Data Analysis
... Check this out: https://omictools.com/metagenomics-category They manage a curated list of bioinformatics tools. From their site: "OMICtools strives to accelerate research in bioinformatics, making tools accessible to everyone and offering a stimulating work environment to assist life scientists ext ...
written 20 months ago by Leonardo Normando60
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Comment: C: Show Progress (Bar?) For Blast+ Query
... Update: I tried the script with an html output, but it didn't worked. Changing # grep -c "^Query= # to # grep -c "Query= # corrects that. I tried other outfmt options, but no luck :( The script will work on default blast+ output (outfmt=0) and html format. Also, I changed the end of script a bit t ...
written 7.7 years ago by Leonardo Normando60
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Comment: C: Show Progress (Bar?) For Blast+ Query
... That did the trick :) ...
written 7.7 years ago by Leonardo Normando60
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Comment: C: Show Progress (Bar?) For Blast+ Query
... Sorry for the delay, I liked RM's approach but there is a problem: the blast output file does not update itself until the program stop working, therefore it's not possible to retrieve progress information in real time. Any suggestions? ...
written 7.7 years ago by Leonardo Normando60

Latest awards to Leonardo Normando

Voter 20 months ago, voted more than 100 times.
Student 2.7 years ago, asked a question with at least 3 up-votes. For Show Progress (Bar?) For Blast+ Query
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Show Progress (Bar?) For Blast+ Query
Supporter 7.5 years ago, voted at least 25 times.

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