Moderator: a.zielezinski

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a.zielezinski9.6k
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Andrzej Zielezinski

Posts by a.zielezinski

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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 8 months ago by a.zielezinski9.6k
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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 9 months ago by a.zielezinski9.6k
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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 9 months ago by a.zielezinski9.6k
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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 9 months ago by a.zielezinski9.6k
0
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1
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Comment: C: ID query with entrez -- invalid ID - rllib.error.HTTPError: HTTP Error 400: Bad
... Thank you for sharing! ...
written 9 months ago by a.zielezinski9.6k
4
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490
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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 9 months ago by a.zielezinski9.6k
3
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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 months ago by a.zielezinski9.6k
1
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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 9 months ago by a.zielezinski9.6k
1
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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 10 months ago by a.zielezinski9.6k
5
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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 10 months ago by a.zielezinski9.6k

Latest awards to a.zielezinski

Good Answer 17 hours 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 5 days 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 8 days 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
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Making A Consensus Phylogenetic Tree
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Scholar 6 weeks ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: How To Separate A List Of Genomics Regions Into Several Disjoint Subsets
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Scholar 4 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Great Question 6 months ago, created a question with more than 5,000 views. For Hmmsearch (Hmmer) Tblout Format
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 9 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Scholar 10 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: biopython pairwise2 result to a file
Scholar 10 months ago, created an answer that has been accepted. 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
Scholar 12 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Scholar 12 months ago, created an answer that has been accepted. For A: biopython pairwise2 result to a file
Good Answer 13 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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