pyfastx
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lmdu
a python package for fast random access to sequences from plain and gzipped FASTA/Q files
Hi, is it possible to open multiple fastq files (and process) at the same time using pyfastx.Fastq? With file handle, I could do something like this: ``` with gzip.open(R1_fastq_file, 'r')...
Hi Ive got an unaligned BAM file from a pac bio long-read run which ive converted to a fq using bedtools. I am then trying to use pyfastx to play...
**Primary change** This fix changes the behavior of Sequence objects created inside for loops over Fasta objects, so that they don't unexpectedly change when used repeatedly. EXAMPLE: 1) Create a...
Added linux aarch64 wheel build support. related to #34. @lmdu, could you please review this PR?
I loaded a fasta file containing 4542 sequences with average length of 2.5kb, however only 4539 sequences were in the pyfastx.Fasta object. ``` fa = pyfastx.Fasta('assembly.fasta') fa['contig_4540'] # keyError ```...
Hello, I wanted to use pyfastx for some ENCODE analysis and tried to use the `Fasta` class on the GRCh38 reference found [here](https://www.encodeproject.org/data-standards/reference-sequences/) (more info [here).](https://www.encodeproject.org/files/GRCh38_no_alt_analysis_set_GCA_000001405.15/). When I iterate through...
eg ``` for read in pyfastx.Fastq(f'{u}.fastq'): read_id = read.name # read_id = original read_id plus phred ```
Using pyfastx version 0.8.4, I tried iterating over records but the "comment" attribute is not reset. Is there a safer way to iterate (I would like not to assume FASTA...
Hello! I made a trivial function that returns a sequence from a Fasta class expecting it to return an object of the Sequence class. However, it returns meaningless and different...
Problem --------- On aarch64, pip install pyfastx builds the wheels from source code and then install it. It requires user to have development environment installed on his system. also, it...