User: liorglic

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liorglic280
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Posts by liorglic

<prev • 67 results • page 1 of 7 • next >
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What happens during Blast DB creation?
... Hello, I am curious to know what happens (algorithmically) during the creation of blast DBs, for example when we run "makeblastdb" on the command line. I understand that there is some masking and indexing involved, but would like more details. Can anyone explain or suggest some resource explaini ...
blast written 9 days ago by liorglic280
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Comment: C: Extract last exon annotation from each mRNA
... Sorry - my bad. Fixed. ...
written 13 days ago by liorglic280
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Comment: C: Extract last exon annotation from each mRNA
... How about something like this? import GFFutils G = GFFutils.GFFDB('dm3.db') for gene in G.features_of_type('gene'): exons = list(G.children(gene, featuretype='exon')) first_3_exons = exons[:3] last_3_exons = exons[-3:] ...
written 14 days ago by liorglic280
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Comment: C: Extract data from a large bed file
... Since you are interested in low-level text processing, I'd say that awk or basic python would be the way to go. Higher-level parsers provide useful shortcuts, but usually at the cost of speed. ...
written 14 days ago by liorglic280
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Answer: C: Extract last exon annotation from each mRNA
... What have you tried so far? Let's see the code... ...
written 14 days ago by liorglic280
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Comment: C: COVID19 testing - can we/should we use NGS?
... Apparently I'm not the only one who had this idea: https://docs.google.com/document/d/1kP2w_uTMSep2UxTCOnUhh1TMCjWvHEY0sUUpkJHPYV4/edit?usp=drivesdk Still unclear if it's a good one though... ...
written 15 days ago by liorglic280
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Answer: C: Turning VCF INFO Column into a dataframe
... In python you can use the [PyVCF package][1]. It parses VCF files, returning INFO data as a dict, so it should be fairly simple to convert to pandas data frame. [1]: https://pyvcf.readthedocs.io/en/latest/ ...
written 15 days ago by liorglic280
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Answer: A: regex for select dna sequence
... The reason your code doesn't work is that you are iterating on file lines but trying to search multiple lines at the same time. There are multiple ways around this, but I'd say the most elegant one is to use a ready-made library to parse fasta files such as Bio.SeqIO. if all you need is to remov ...
written 15 days ago by liorglic280
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Comment: C: Average length of each exon and intron
... There are quite a few issues with your code, the main one being that you are not separating your analysis by mRNA, which is necessary if you want to get the average length of the 1st, 2nd, 3rd exons etc, across all mRNAs. In general, it is better to use existing libraries for parsing specific format ...
written 15 days ago by liorglic280
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Answer: A: Counting how many transcripts per gene in gtf file
... Here is a quick option with awk: awk -F "\t" '$3 == "transcript" {split($9,a,";"); print a[1]}' | sort | uniq -c but you may also want to check out a library that parses gtf/gff in your favorite programming language. ...
written 16 days ago by liorglic280

Latest awards to liorglic

Scholar 23 days ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: Removing small contigs from fasta files
Scholar 5 weeks ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Removing small contigs from fasta files
Scholar 3 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Scholar 4 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Removing small contigs from fasta files
Popular Question 6 months ago, created a question with more than 1,000 views. For Gene copies vs. gene paralogs - what's the difference
Popular Question 7 months ago, created a question with more than 1,000 views. For Gene copies vs. gene paralogs - what's the difference
Popular Question 8 months ago, created a question with more than 1,000 views. For Pysam (python) problem parsing BAM reference id
Scholar 14 months ago, created an answer that has been accepted. For A: What's the right way to submit a genome assembly to NCBI?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Where can I find a small NGS raw data set?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Pysam (python) problem parsing BAM reference id

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