Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
Questions tagged [pysam]
50 questions
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Python- Can not install HTSEq
I can not install HTSeq in python 3.6.1.
When I try to install, it gives me this error:
"AttributeError: 'NoneType' object has no attribute 'encoding'[0m 2"
user6941992
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2 answers
Detect large deletions from CIGAR string
I am new to sequence analysis and I'm doing some exercises to help me learn to use pysam and samtools for WGS data analysis. One thing I would like to do is to detect (rather large) deletions from 2D Oxford nanopore data (large reads). For this…
Sigurgeir
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Multiprocess, various process reading the same file
I am trying to simulate some dna-sequencing reads, and,in order to speed-up the code, I am in need to run it on parallel.
Basically, what I am trying to do is the following:I am sampling reads from the human genome, and I think that one the two…
Praderas
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BAM file: getting all reads on certain position with pysam
I have a BAM-file with on a certain position 520817 reads (as seen in IGV). However, when I use pysam to get the read name and the associated nucleotide on a specific position, I do not get that amount by far (only get around 7000 reads). I think I…
Michaël Noë
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An issue about pysam installation
It's linux, using conda to install pysam, and pip install pysam keep failing.
After successful installed pysam,
pysam shows in conda list and appears in anaconda2/pkgs/
but when import pysam in python 2.7.12, it failed by Traceback (most recent…
Lucas Lau
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2 answers
Is there a way to save an entire "alignment field/column" into a NumPy array using Samtools?
In the SAM format, each alignment line represents the linear alignment of a segment, and each line have 11 mandatory fields, i.e. QNAME, FLAG, RNAME, POS, MAPQ, etc.
Let's say I wanted a NumPy array of all "QNAMES" in a given BAM file. Or, one…
ShanZhengYang
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Upgrading python pacakge in python2.7
I am new to python. I need to run a python script(riboplot) in python2.7 which requires the package "pysam_0.8.4" to run. In my python2.7, when I checked the version
import pysam
pysam.__version__
it showed me '0.7.5'. But in my python3.4, it is…
Carol
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1 answer
How to use pysam.view to emulate all functions of samtools view
I am trying to use pysam.view() to filter out certain alignments from a BAM file. The problem I am facing is how to include several regions in the filter.
pysam.view() emulates the samtools view command which allows one to enter several regions…
Chaus
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1 answer
Error message when use Python multiprocessing
I need to convert a very huge .bam file to .bed file, although I found a solution by using bedops's bam2bed parallel, that parallel support SEG and gnuParallel, the two clusters I can access only support slurm and torque schedulers, and I do not…
Fei Yuan
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2 answers
Accessing Bam file at particular location using Pysam
I have a given chromosome number and location (chr1 and location 1599812). I want to use the pysam module of python to access the bam file to obtain read numbers information for only that particular region chr1 and location 1599812. I have tried…
BioInformatician
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1 answer
Converting nested tuple 0 into row in matrix
I'm tring to make a code to simulation a wind turbine but it doesn't work, the error message that diplay said me that there is a worst tuple in my dictionnary but i've verified that several times but ther is no error. I need help.
Here is the code…
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Error in installing of pysam (error to build HSTlib) during of CNVkit installation
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I install the Linux server by VMware and try to install CNVkit but during the build of wheel in installation of pysam we have upper mentioned error. I had tried to install pysam separately but the same error was happened…
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PySAM import failure on python3.11 macbookPro M2
I am working with a macbook Pro M2, I have installed pyhton3. 11, and I have installed PySAM using "pip install PySAM" in the terminal. However, I cannot use and import PySAM in my python environment. I have tried it with jupyter and visual studio…
Taslimi
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Pysam view yield reads one at a time
I'm trying to using pysam to filter a .bam file for mapping quality and excluding flags.
I know I can use .fetch() and iterate through reads that way, but I'm guessing it's faster to first use pysam.view()
However, when I try this on a large .bam,…
rbierman
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MapDamage [E::fai_retrieve] Failed to retrieve block: unexpected end of file, in snakemake pipeline
I don't know what to check next to solve the issues. I trie to re install mapdamage et transforme the .bam to .sam to check the file which seems fine.
And I still have the issue :
rule MapDammage:
input: /*/hg19.fa,…
angelina.Z.H
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