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Dev #226

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merged 16 commits into from
Jun 4, 2024
Merged

Dev #226

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01eee9d
update bedpe file format
atancoder Apr 24, 2024
1b1330f
Merge pull request #219 from broadinstitute/update_bedpe_generation
atancoder Apr 24, 2024
62dd759
update bedpe file creation
atancoder Apr 30, 2024
f21fc57
Merge pull request #220 from broadinstitute/update_bedpe
atancoder Apr 30, 2024
0e814de
clean up hic processing code
atancoder May 2, 2024
dc1dde7
support adaptable search space for hic
atancoder May 2, 2024
22d243e
only support 5kb res for hic
atancoder May 3, 2024
93f8533
Update getting_started.rst
atancoder May 6, 2024
14d2176
Merge branch 'dev' into update_hic
atancoder May 8, 2024
11f7b27
Merge pull request #221 from broadinstitute/update_hic
atancoder May 8, 2024
d2cca03
remove default for hic_psuedocount_distance in predict.py since it's …
atancoder May 9, 2024
f3b9bff
utilize amazon link as the encode link leads to a segfault in CircleCI
atancoder May 29, 2024
b0c7ecb
Merge pull request #224 from broadinstitute/update_test_hic
atancoder May 29, 2024
6ddc6ce
update release conda env
atancoder May 30, 2024
2f73fc2
Update circleci config.yml
atancoder Jun 4, 2024
8a43013
Merge pull request #225 from broadinstitute/atancoder-patch-1
atancoder Jun 4, 2024
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1 change: 1 addition & 0 deletions .circleci/config.yml
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Expand Up @@ -21,6 +21,7 @@ jobs:
# The executor is the environment in which the steps below will be executed
docker:
- image: condaforge/mambaforge
resource_class: large # 8GB of memory
# CircleCI will report the results back to your VCS provider.
steps:
- checkout
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3 changes: 2 additions & 1 deletion docs/usage/getting_started.rst
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Expand Up @@ -15,6 +15,7 @@ Installation
- Make sure you're not using strict channel priorities: ``conda config --set channel_priority flexible``. Otherwise, you may encounter package conflicts later when installing abc.
- To install mamba: ``conda create -n mamba -c conda-forge mamba -y``
- We recommend mamba as using conda can take 1hr+ for setup
- See troubleshooting page if you run into issues


Setup Conda Environment
Expand Down Expand Up @@ -123,7 +124,7 @@ biosamples config is a tsv separated file with the following columns
- If you dumped hic into a directory via JuicerTools, use ``juicebox``
- If you have a bedpe file for contact, it should be a tab delimited file containing 8 columns (chr1,start1,end1,chr2,start2,end2,name,score)
#. HiC_resolution (int)
- Recommended to use 5KB (kilobases)
- Currently only 5KB (kilobases) is supported
- 5KB means dna regions are bucketed into 5KB bins and we measure contact between those bins
#. alt_TSS (optional; not recommended to fill)
- Alternative TSS reference file
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2 changes: 1 addition & 1 deletion tests/config/test_biosamples.tsv
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@@ -1,3 +1,3 @@
biosample DHS ATAC H3K27ac default_accessibility_feature HiC_file HiC_type HiC_resolution alt_TSS alt_genes
K562_chr22 example_chr/chr22/ENCFF860XAE.chr22.sorted.se.bam example_chr/chr22/ENCFF790GFL.chr22.sorted.se.bam DHS https://www.encodeproject.org/files/ENCFF621AIY/@@download/ENCFF621AIY.hic hic 5000 example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.TSS500bp.bed example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.bed
K562_chr22 example_chr/chr22/ENCFF860XAE.chr22.sorted.se.bam example_chr/chr22/ENCFF790GFL.chr22.sorted.se.bam DHS https://encode-public.s3.amazonaws.com/2022/05/15/0571c671-3645-4f92-beae-51dfd3f42c36/ENCFF621AIY.hic hic 5000 example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.TSS500bp.bed example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.bed
K562_chr22_tagAlign example_chr/chr22/chr22.sorted.tagAlign.gz ATAC example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.TSS500bp.bed example_chr/chr22/RefSeqCurated.170308.bed.CollapsedGeneBounds.chr22.hg38.bed
2 changes: 1 addition & 1 deletion tests/test_predictor.py
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Expand Up @@ -7,7 +7,7 @@
from predictor import add_hic_from_hic_file
import pandas as pd

HIC_FILE = "https://www.encodeproject.org/files/ENCFF621AIY/@@download/ENCFF621AIY.hic"
HIC_FILE = "https://encode-public.s3.amazonaws.com/2022/05/15/0571c671-3645-4f92-beae-51dfd3f42c36/ENCFF621AIY.hic"

# this file has 3k rows of E-G pairs with valid contact values
# contact values were generated from the original doubly stochastic method
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3 changes: 2 additions & 1 deletion workflow/envs/abcenv.yml
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Expand Up @@ -13,6 +13,7 @@ dependencies:
- numpy
- pandas
- pybigwig
- pulp<2.8 # Pin pulp <2.8 for snakemake: https://github.com/snakemake/snakemake/issues/2607
- pip
- pyarrow
- pyranges
Expand All @@ -35,4 +36,4 @@ dependencies:
- zlib
- pip:
- sphinx_rtd_theme
- hic-straw
- hic-straw
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