pip error code 1 when installing pyopenssl

Hi I am trying to install pyopenssl so i can use scrapy. When i run the installation i get this error with pip. I also get the same error when trying to install scrapy... Command python setup.py...

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...

How to cache reads?

I am using python/pysam to do analyze sequencing data. In its tutorial (pysam - An interface for reading and writing SAM files) for the command mate it says: 'This method is too slow for...

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...

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...

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...

Keep getting error incompatible library version libchtslib.so requires version 9.0.0 or later, but libcurl.4.dylib provides version 7.0.0

I am trying to install a program called metaBIT. I was able to add it to my PATH. But when I execute: metaBIT -h It errors and gives me this: Traceback (most recent call last): File...

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...

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...

Conda build and cython problems

I am trying to create a conda package to distribute a python tool. Part of the tool is cythonized, and it works perfectly using python setup.py install. I create the tar properly but when I try...

unable to execute 'x86_64-conda_cos6-linux-gnu-gcc': No such file or directory (pysam installation)

I am trying to install pysam. After excecuting: python path/to/pysam-master/setup.py build This error is produced: unable to execute 'x86_64-conda_cos6-linux-gnu-gcc': No such file or...

Iterate overs values in nested list

I'm working on scientific data and using a module called pysam in order to get reference position for each unique "object" in my file. In the end, I obtain a "list of lists" that looks like that...

Python error: OSError: error when opening file `all_fprau.fasta`. Fasta file too large?

I have a script that searches through a csv file and a fasta file and any ID's that are in both files will be used to extract the fasta sequence from fasta file. It looks like this: import...

Changing an orientation of a reverse sequence in the fasta file doesnt work

I am trying to get the reverse sequences orientated correctly in a file. This is the code: import os import sys import pysam from Bio import SeqIO, Seq, SeqRecord def main(in_file): out_file...

Can't install pysam with pip in Python 3.6

Macbook Mac OSX 10.12.6 Python 3.6.2 cython 0.28.5 pip 18.0 I'm trying to install pysam: pip3 install pysam It keeps hitting an error at: creating...

"ImportError: No module named oldnumeric" when running PMV from mgltools

I installed a tool called mgltools using following command conda install mgltools When I tried to test the installation using command pmv I got following error setting PYTHONHOME environment Run...

Command "python setup.py egg_info" failed with error code 1 (Anaconda/Windows)

I am running Anaconda, trying to install nanopack with pip install nanopack. It fetches all the packages, but then I get the following: (base) C:\WINDOWS\system32>pip install nanopack Collecting...

Passing an iterator to dask.delayed function

I'm trying to pass an iterator over a (non-standard) file-like object to a dask.delayed function. When I try to compute(), I get the following message from dask, and the traceback...

snakemake script access to stdin / stdout for stream processing

For a Snakemake workflow, I need to manipulate tags in many BAM files, and would like to process these by piping them through a script (using the Snakemake script: directive). The specific way I'm...

CondaValueError: Malformed version string '~': invalid character(s)

I'm getting a Malformed version string error with my conda. I have no idea how to debug this or how to check it. Can anyone help? GitHub has talked about the issue but I haven't seen any...

Specify setup time dependency with `--global-option` for a python package

I'm trying to package a python library that has setup-time (and also run-time) dependencies: it imports the modules so that the modules can inform the setup process of the location of some...

How do I resolve a UnsatisfiableError when installing deeptools?

I am trying to install deeptools on an Anaconda2 prompt for Python 3.7 and 2.7 by following this tutorial. First, I got an environment error which I solved by running the following: $ conda create...

Pip install fails at building wheel at subpackage?

Somewhat a beginner at coding. I was looking to install a package using pip install that I was able to get before I updated my python (currently have Python 2.7.16 and 2.8.0 on my Mac). The...

Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.** while installing gumpy

I am trying to install gumpy on my computer but I ran into this Error: ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. I use pip...

Why does installing pysam python package fail?

I'm new to python and running the command: pip install pysam Which results in: Collecting pysam Using cached...

Command errored out with exit status 1: Python setup.py [...] When trying to install Pysam

I have been troubleshooting this issue for several days now and have had to draw the conclusion that i need help from you guys! Info: Python version: 3.8.2 Pip version: 20.0.2 Updated...

extract lines from bam file

I have a bam file that looks like this: samtools view pingpon.forward.bam |...

How to interpret conda package conflicts?

I am attempting to create a conda environment with 3 packages and a specific python version and get the following output: $ conda create -n testing_junk -y instrain awscli samtools...

Deeptools cannot find file that exists

An intern of mine is trying to use deeptools' bamCoverage function, and it throws a '/my/dir/data.bam' file does not exist error, despite the file being there. Yes, the file does exist, we can...