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Enlarge the sampling range for column determination in FilterGTF script. #1127

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Nov 20, 2023
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Enlarge the sampling range for column determination in FilterGTF script. #1127

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Enlarge the sampling range for column determination in FilterGTF script.
MatthiasZepper Nov 20, 2023
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MatthiasZepper Nov 20, 2023
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MatthiasZepper Nov 20, 2023
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Update CHANGELOG.md
pinin4fjords Nov 20, 2023
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4 changes: 2 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -7,8 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Enhancements and fixes

- [PR #1126](https://github.com/nf-core/rnaseq/pull/1126) - Fixes error when transcript_fasta not provided and skip_gtf_filter set to true
- [#1125](https://github.com/nf-core/rnaseq/issues/1125) - Pipeline fails if transcript_fasta not provided and skip_gtf_filter = true
- [[PR #1126](https://github.com/nf-core/rnaseq/pull/1126)] [[#1125](https://github.com/nf-core/rnaseq/issues/1125)] - Pipeline fails if transcript_fasta not provided and `skip_gtf_filter = true`.
- [[PR #1127](https://github.com/nf-core/rnaseq/pull/1127)] - Enlarge sampling to determine the number of columns in `filter_gtf.py` script.

## [[3.13.1](https://github.com/nf-core/rnaseq/releases/tag/3.13.1)] - 2023-11-17

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4 changes: 2 additions & 2 deletions bin/filter_gtf.py
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Expand Up @@ -23,14 +23,14 @@ def extract_fasta_seq_names(fasta_name: str) -> Set[str]:
def tab_delimited(file: str) -> float:
"""Check if file is tab-delimited and return median number of tabs."""
with open(file, "r") as f:
data = f.read(1024)
data = f.read(102400)
return statistics.median(line.count("\t") for line in data.split("\n"))


def filter_gtf(fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_id_check: bool) -> None:
"""Filter GTF file based on FASTA sequence names."""
if tab_delimited(gtf_in) != 8:
raise ValueError("Invalid GTF file: Expected 8 tab-separated columns.")
raise ValueError("Invalid GTF file: Expected nine tab-separated columns.")

seq_names_in_genome = extract_fasta_seq_names(fasta)
logger.info(f"Extracted chromosome sequence names from {fasta}")
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