gfapy

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Feature: converting graphs to GFA

1

Thank you for your work on `gfapy`; In the documentation, I could not find a function to convert well-known graph data structures like `igraph` or `networkx` to `gfa`. Assume that...

aafshinfard

Hello, I am encountering an error when attempting to use the functions `graph.is_cut_segment` and `graph.remove_dead_ends` where it appears that the function attempts to interate over a `SegmentEnd` and fails: EG...

mir-cat

Optimization: add ability to ignore sequences when loading a GFA file

6

Thank you for your work on Gfapy! I have a very large GFA file (over 3 GB), including ~80k segments that I'd like to load using Gfapy. Although this graph...

fedarko

Setting 'or' tag in merge_linear_paths

1

Hi Giorgio, Thanks for the great library! I came across an issue when using `merge_linear_paths` with `enable_tracking=True`. Not sure if it's a general problem or maybe a version incompatibility? The...

W-L

Update integer.py to parse integers in exp notation

1

When integer value is given in exponential notation, python doesn't parse it as an integer resulting in not validating the `gfa` file. Casting to `float` and then to `int` resolves...

msgr0

Is it possible to keep coverage/count information when using `merge_linear_paths`? E.g., this is snippet of my starting graph which has FC tags: ``` S 35 TATTTTTATTAGAGACCTTGATTCCGATAATATTCATGTTGTATTAGCCGATTTTGGTCTAGCCAAAGCAAGTATGGGTTCAGTTGACAGATCCTATGCTGGCACTCCTTTATACATGTCTTTAGAACTCGCAACCGGAGGAAAGTACAGTTTCAATACCGATATCTATTCATTGGGAGTGGCTATCTATCAAATCATGACCAAAGACACAACCACAGCTGTCAGTCACATGTTTATTTCGAATAGAGAGGAAGAAGCAATTGATAAATTAACAAAGGAAATGGAAAAATCAGGAAATTATTCAACAACATTGATTAATATTTGTTTATCTATGCTGGAGAAGGATGCCAGTAAGAGACCAAGTGCCAAGCAAATCCTTTCCAATACTTTCTTGGAAGATATTCTCATCACACCAACAGAATAAACAATTTCTTGTGTTTTACCGCTGAAGTTAACCGTTAGAATTATAATAATTTTATTTTTCACAACAAAAAAAACAAGCCAACAACAATAGAGCGGGTGCAAACTCGGGTGTATCTACCGTTTTTCGTTTCTGAAAACGACTTTCGTTTTTGTTCGTGTTTGAATGAAGATTTTTGGTGTTTCTTTCAAATTCATACAAGATCGTTTTTCGTTTTTGTAAAAAGTTAGAAAAATACGAAAACGTGGCAAGTTGCACCTGCTCTAATGTGGGCAACAAACTTGAGGTTACCATTACCTTCTTGAATGATCATCAGAAGATTATTCATCTTCGCTTACCATCAGAGATCTGATTATTAACCGCTCTTGACTGTCAACTGAGATTTGGCAGGTGAAATTCAGTTTTCACATTCGCCAAAAGAAAATGAAGATAAATGATGATGAATTGAATAATTCTTGAATTTCTTCCTACGGATAGCTATGCATCATTCTCACATATCAATAGGCAGTGTCAATCTATTCTTGTTTCGGAAAAACCAAACTTTTGGAAACAGAAAAAGAGTGAATATGATAGAACTATTGCCAACCAAGAACGATACCTCGACCATGTTATTGATACAATGACAAGAAATGCTTCTAAGAACAATTATTGTTTATTTGCTTGTTTTGTCGGGATGTTGTTTTCGTTTCTTGTGTTTTTACCAGCATTTATGATCATGGTGATTATGGCATCTAGTTCCCTTTCAGGAAATATATTGAATTGTGAGAGGAATGTTTCTTCTATTCAAGTTTTGAATAGAACTATTGAAAGGGTTTCTTATCCAGGATGTGTAGAATGTAACACAATTTGGAATACTAGTTGCAATAATTTCAATGTTATGCCATGTTGTCAACCAAATAATAGTTATTCTTCAATTTTCTCATATGAATGCAATGTAACTGAATGCATTAAGGAAAATTATCAAGATGGACCTCTCAGATGTCGAGTAATTAGTTACAACAACAAAAAAGGGCCATCCACATATTCACTAGTCATTTACAAACCAGAAAGCAATTATTCAGGGTCTATAGGACTATTATCTGGTTAGCTACCAATACTTATGATTTGAAAGTTTAGTCAGATTACTGAAATACTGACTTTATTTCACTAACAACACGTAGGTCGGCAATGTGATTCCTTCTTCATAATTGAGTATTAATCGTACGGTATTTGCAAGTAAATAATAACTAATAATGGTCAATTAACAAAATATTAAATAAATTATTTAAAAAAAATGAAAAGAAGCAGAGAGGAGGAACCTGCTGTTACCAATACATCATGTACTGATCAAAGTAATACAAGTTCCGATCCTCTCTTGGAAACGAATCTAAAAAAACAAGTGACTGGCAATATTT ll:f:44.5 FC:i:80768 kl:f:44.5 S...

jamiemcg

Improve documentation on Methods to access segments, edges, etc. by id

7

Thanks @ggonnella for a great library! This is more of a question than an issue. I don't see any documentation on how I can access particular segments and edges in...

nhansen

gfapy.error.NotFoundError: A link equivalent to ... does not exist

1

Dear Giorgio Thanks for your nice library! I get this exception: ``` gfapy.error.NotFoundError: A link equivalent to: L edge_2 - edge_1 + * does not exist, but is required by...

MrTomRod

Thanks for the great library! Running gfapy 1.2.3 on the following file: [test.gfa.gz](https://github.com/user-attachments/files/17238218/test.gfa.gz) ```python g = gfapy.Gfa.from_file("test.gfa", vlevel=3) gfa_line = g.line("k141_11431") gfa_line.disconnect() ``` Based on the [docs](https://gfapy.readthedocs.io/en/latest/tutorial/gfa.html?highlight=disconnect#removing-lines), I expected all...

schorlton-bugseq

can it be used to rename contig names in gff file?

gunjanpandey