mirror of
https://github.com/KosinskiLab/AlphaPulldown.git
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fff63051b4
* Harden MMseqs species ID resolution fallback * Reorganize tests for CPU coverage CI * New * Fix function coverage checker def-line false positives * Expand unit coverage for helper and backend manager utilities * New. * New. * Expand unit coverage for template and post-processing helpers * Expand unit coverage for objects.py edge cases * Publish HTML coverage reports via GitHub Pages * Add CPU unit coverage for AlphaFold3 backend helpers * Reorganize tests and expand backend coverage * Reset shared test flags between cases * Expand AF3 prepare_input unit coverage * Cover AF3 and truemultimer feature creation * Test AF3 multimer MSA translation paths * Cover AF3 duplicate-residue multimer fallback * Cover AF2 resume and postprocess edge paths * Cover AF3 template mmCIF preparation * Test small script entry points * Expand workflow and ModelCIF test coverage * Add backend extras and install guide * Clarify AF3 backend installation path * Stabilize cluster GPU test runners * Document AF3 CMake SQLite hints * Simplify backend installation guide * Align AF3 install with working cluster env * Backfill typing dataclass_transform for AF2 * Pin TensorFlow for cluster installs * Fallback AF2 relax when CUDA OpenMM is unavailable * Raise AF3 default minimum bucket size * Simplify backend cluster installation guide * Fix AF3 wrapper JSON output isolation * Fix AF3 JSON wrapper outputs and MMseqs ID parsing * Fix CI entrypoint stub and Python 3.8 typing * Document release readiness test gates
45 lines
1.1 KiB
Python
Executable File
45 lines
1.1 KiB
Python
Executable File
#!/usr/bin/env python3
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import sys
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from itertools import groupby
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import re
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"""
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Rename Uniprot names in FASTA file to uniprot IDs
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(split by | and take second element)
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"""
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def fasta_iter(fh):
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"""Return iterator over FASTA file with multiple sequences.
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Modified from Brent Pedersen
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Correct Way To Parse A Fasta File In Python
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given a fasta file. yield tuples of header, sequence
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:param fh: File Handle to the FASTA file
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:return: 2-element tuple with header and sequence strings
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"""
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# ditch the boolean (x[0]) and just keep the header or sequence since
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# we know they alternate.
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faiter = (x[1] for x in groupby(fh, lambda line: line[0] == ">"))
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for header in faiter:
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# drop the ">"
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headerStr = header.__next__()[1:].strip()
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# join all sequence lines to one.
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seq = "".join(s.strip() for s in faiter.__next__())
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yield (headerStr, seq)
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out_lines = []
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with open(sys.argv[1]) as f:
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for headerStr, seq in fasta_iter(f):
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items = re.split(r"[ |]", headerStr)
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out_lines.append(f'>{items[1]}')
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out_lines.append(seq)
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print("\n".join(out_lines))
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