User: frcamacho

gravatar for frcamacho
frcamacho190
Reputation:
190
Status:
Trusted
Location:
United States
Last seen:
4 weeks, 1 day ago
Joined:
5 years, 11 months ago
Email:
c**************@gmail.com

Posts by frcamacho

<prev • 43 results • page 1 of 5 • next >
0
votes
2
answers
3.4k
views
2
answers
Comment: C: parsing hammer 2.3.2 results using biopython
... Hi, this script works with hmmer3-text format ([https://lifebit.gitbook.io/cloudos/pipelines-documentations-and-examples-1/docker-pipelines-and-tools/hmmer][1]) Is this the format you are trying to parse? If not, SearchIO has the following options, you can change the code to other forms > for re ...
written 4 weeks ago by frcamacho190
1
vote
1
answer
212
views
1
answers
Comment: A: esearch discrepancies using bash commands vs direct esearch command line
... This is also a heads up for those using esearch. The esearch command consumed the entire file (stdin), hence I got output only for the first line. I used `IFS=$'\n'; for next in $(cat file); do ..; done` to get it to work with a file as input. ...
written 8 months ago by frcamacho190
1
vote
1
answer
212
views
1
answers
Comment: C: esearch discrepancies using bash commands vs direct esearch command line
... Thank you Pierre! Updated code and it works! cat test-file.txt | while read p; do echo $p; esearch -db gene -query "$p[Gene name] AND Homo sapiens[ORGN] AND alive[Prop]" | efetch -format tabular > results.txt; done; ...
written 8 months ago by frcamacho190 • updated 8 months ago by RamRS30k
8
votes
1
answer
212
views
1
answer
esearch discrepancies using bash commands vs direct esearch command line
... Hi there, I am using esearch to query symbols within a file against NCBI. I am using the following command cat test-file.txt | while read p; do echo $p; esearch -db gene -query '"$p"[Gene name] AND Homo sapiens[ORGN] AND alive[Prop]' | efetch -format tabular > results.txt; done; In the tes ...
ncbi entrezdirect esearch written 8 months ago by frcamacho190
1
vote
0
answers
238
views
0
answers
Comment: C: Pheatmap or Heatmap3 ?
... I used to use pheatmap, but I agree with @RamRS. ComplexHeatmap brought R heatmaps a needed makeover. You should take a look at the complete reference for ComplexHeatmap to get you started. > https://jokergoo.github.io/ComplexHeatmap-reference/book/introduction.html ...
written 9 months ago by frcamacho190
0
votes
0
answers
200
views
0
answers
Comment: C: prinseq and sickle
... Can you please attach the conda commands you used to run the installation? For example; > `conda install -c bioconda prinseq` Also, any error messages you received. Did you install prinseq and sickle within a conda environment? If so, make sure you are activating your environment before callin ...
written 9 months ago by frcamacho190
0
votes
0
answers
878
views
0
answers
Comment: C: Query UniProt database with Mnemonic identifier
... Update: I was able to convert using http://www.uniprot.org/mapping/ from UniProtKB AC/ID to UniProtKB. This works, but would like to be able to implement some code. Thanks! ...
written 2.4 years ago by frcamacho190
2
votes
0
answers
878
views
0
answers
Query UniProt database with Mnemonic identifier
... I have a list of UniProt Names, Mnemonic identifier of a UniProtKB entry. I am trying to query the UniProt database to retrieve the information of that entry that matches the mnemonic identifier and following filtering: Human taxa and Reviewed. Is there a way to do this in R? What I currently am doi ...
R uniprot written 2.4 years ago by frcamacho190
4
votes
2
answers
941
views
2
answers
Retrieve sequences that generated a HMM profile
... Hi All, I have HMM profiles but the raw sequences or multiple sequence alignments are not available. I saw the tool `hmmemit`, but this randomly generates sequences that match a given profile HMM. I do not want random sequences. Is there a way to obtain sequences or multiple sequence alignment tha ...
hmmer written 2.7 years ago by frcamacho190 • updated 2.7 years ago by Jean-Karim Heriche23k
0
votes
1
answer
2.1k
views
1
answers
Comment: C: Help with CD-hit commands for DNA sequences
... Which version are you running? I am running 4.6 (built on Jul 29 2016) ...
written 3.6 years ago by frcamacho190

Latest awards to frcamacho

Appreciated 6 months ago, created a post with more than 5 votes. For A: Continuously add lines to ggplot with for loop
Popular Question 6 months ago, created a question with more than 1,000 views. For Tabular fields of DIAMOND.m8 file
Supporter 8 months ago, voted at least 25 times.
Great Question 11 months ago, created a question with more than 5,000 views. For Tabular fields of DIAMOND.m8 file
Great Question 15 months ago, created a question with more than 5,000 views. For Tabular fields of DIAMOND.m8 file
Great Question 15 months ago, created a question with more than 5,000 views. For Conditionally merge columns using Pandas
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Continuously add lines to ggplot with for loop
Epic Question 21 months ago, created a question with more than 10,000 views. For Conditionally merge columns using Pandas
Popular Question 23 months ago, created a question with more than 1,000 views. For Tabular fields of DIAMOND.m8 file
Great Question 2.6 years ago, created a question with more than 5,000 views. For Conditionally merge columns using Pandas
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Tabular fields of DIAMOND.m8 file
Scholar 3.4 years ago, created an answer that has been accepted. For A: Sublime Text 2: Output Error After I Installed Anaconda
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Conditionally merge columns using Pandas
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Conditionally merge columns using Pandas
Popular Question 4.1 years ago, created a question with more than 1,000 views. For parsing hammer 2.3.2 results using biopython
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Bulk downloading IMG gene ID information
Scholar 4.2 years ago, created an answer that has been accepted. For A: Sublime Text 2: Output Error After I Installed Anaconda
Popular Question 4.2 years ago, created a question with more than 1,000 views. For parsing hammer 2.3.2 results using biopython
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Sublime Text 2: Output Error After I Installed Anaconda
Scholar 5.3 years ago, created an answer that has been accepted. For A: Sublime Text 2: Output Error After I Installed Anaconda

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1978 users visited in the last hour