Moderator: a.zielezinski

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a.zielezinski9.2k
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Andrzej Zielezinski

Posts by a.zielezinski

<prev • 379 results • page 1 of 38 • next >
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Answer: A: python 3.8 'No module named pip'
... Download `get-pip.py` script to install pip: curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py Install pip: python3 get-pip.py Install biopython: python3 -m pip install biopython or pip3 install biopython ...
written 4 weeks ago by a.zielezinski9.2k
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Comment: C: Comparing multiple columns from 2 files using awk, perl or python
... Are sure the output is correct? I think that only "SpoScf_15890 12 2376" fulfils the criteria (start or end in the file1 should be less than in file2, and the difference shouldn't be greater than 1000) ...
written 8 weeks ago by a.zielezinski9.2k
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Comment: C: Comparing multiple columns from 2 files using awk, perl or python
... import sys d = {} for argv in [2, 1]: with open(sys.argv[argv]) as fh: for line in fh: sl = line.split() id = sl[0] st = int(sl[1]) en = int(sl[2]) if argv == 2: d ...
written 8 weeks ago by a.zielezinski9.2k
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Answer: A: Comparing multiple columns from 2 files using awk, perl or python
... Here's Python script: import sys d = {} for argv in [2, 1]: with open(sys.argv[argv]) as fh: for line in fh: sl = line.split() id = sl[0] st = int(sl[1]) en = int(sl[2]) if argv == 2 ...
written 8 weeks ago by a.zielezinski9.2k
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Comment: C: ID query with entrez -- invalid ID - rllib.error.HTTPError: HTTP Error 400: Bad
... Thank you for sharing! ...
written 8 weeks ago by a.zielezinski9.2k
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Answer: A: ID query with entrez -- invalid ID - rllib.error.HTTPError: HTTP Error 400: Bad
... You can modify your script to try downloading the sequence record three times until all fail. If all three attempts fail, skip this record. from urllib.request import urlopen from Bio import Entrez import time Entrez.email = "xxxx@xxxxx.com" IDs = ['AY851612', 'hahdshjhdasd ...
written 8 weeks ago by a.zielezinski9.2k
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Answer: A: Script to obtain human protein sequences by the gene symbols
... You can use XML as query for Ensembl. The following example is for two human gene symbols (**MT-TF** and **TNRC6A**). Format the above XML to one line and download the protein sequences using `wget`. wget -O re ...
written 9 weeks ago by a.zielezinski9.2k
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Answer: C: Makeblastdb refseq viral protein sequence (Blast db v5)
... You can find all viral protein sequences (RefSeq) here: [https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/][1] [1]: https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ ...
written 11 weeks ago by a.zielezinski9.2k
1
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Answer: A: Online pipeline for MSA and NJ tree generation bootstrap supported
... Hi, I highly recommend on-line service [Phylogeny.fr][1]. It performs: - Multiple sequence alignment (Clustal / MUSCLE / T-Coffee / ProbCons) - MSA curation (Gblock / remove positions with gaps) - Tree construction with bootstrap (NJ / Parsimony / Maximum Likelihood / Bayes) - Tree visualizati ...
written 3 months ago by a.zielezinski9.2k
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Answer: A: Reverse translate to all possible codons
... Interesting question - I never thought of it that way. I ended up with something like this: import itertools d = { 'A': ['GCA', 'GCC', 'GCG', 'GCT'], 'C': ['TGC', 'TGT'], 'D': ['GAC', 'GAT'], 'E': ['GAA', 'GAG'], 'F': ['TTC', 'TTT'], 'G': ...
written 3 months ago by a.zielezinski9.2k

Latest awards to a.zielezinski

Scholar 8 weeks ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Scholar 3 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Scholar 3 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Appreciated 5 months ago, created a post with more than 5 votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Scholar 5 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Scholar 5 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Appreciated 6 months ago, created a post with more than 5 votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Scholar 7 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: 200Bp Long Query Returning 201Bp
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Scholar 11 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: 200Bp Long Query Returning 201Bp
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Appreciated 12 months ago, created a post with more than 5 votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Scholar 13 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Appreciated 15 months ago, created a post with more than 5 votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
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