btmartin721 / file_converters

File conversion scripts for DNA sequence data

Hi there!
I'm Bradley T. Martin, PhD
Bioinformatician, Data Scientist,
Evolutionary Biologist, and Population Geneticist

Follow me on Twitter!

✉️ [email protected]

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I earned my Ph.D. in Biological Sciences, focusing on evolutionary biology and population genomics. While pursuing my doctorate, I developed a love for programming. Currently, I work as a bioinformatician and data scientist, specializing in developing machine learning software to process and analyze short-read and long-read genomic data.

I enjoy learning and new challenges and greatly enjoy my work. For personal projects, I am currently developing several new software to implement machine learning into population genomic analyses, which shows promise for resolving long-standing issues involving introgression, species delimitation, and phylogenomics.

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file_converters's Issues

Not reading .loci file correctly

Hello developer,

I am trying to convert a .loci file from ipyrad into fasta alignments, without success.

I get the following warnings:

Warning: skipping read 'loc_13242' because it was < 2 characters long
Warning: skipping read 'loc_13292' because length (0) <= # seed mismatches (0)

Here is a snippet of my .loci file:
aglais.loci.txt

I am very new to bioinformatics and scripts; I am sorry if this is very easy to solve.

Thank you in advance for the help.

Trouble getting loci2phylip and loci2fasta to work

hello,
I have been trying to get each locus as a phylip or fasta for use as inputs for RAxML. When I run :

python3.5 loci2phylip.py --loci ipy002-noTess-reducedBrise_min50perc.loci

I get an error (I am not sure what it means):

Traceback (most recent call last):
File "loci2phylip.py", line 81, in
for aln, lcount, icount, slen in locusGenerator(fin, locus_num):
File "loci2phylip.py", line 43, in locusGenerator
yield locus, locus_count, ind_count, seq_len
UnboundLocalError: local variable 'seq_len' referenced before assignment

when I tried the same file for loci2fasta it produced empty fasta files.

do you know what could be the issue?