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rnmitchell
commented
Jul 18, 2025
lusSTR/workflows/strs.smk
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Comment on lines
77
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94
| system = os.name | ||
| if system == "nt": | ||
| shell("md logs\\{dt}\\Input\\") | ||
| shell('copy "{log}" logs\\{dt}\\') | ||
| shell("copy config.yaml logs\\{dt}\\") | ||
| new_file = input_name.replace("/", "\\") | ||
| if os.path.isdir(input_name): | ||
| shell('xcopy "{new_file}" logs\\{dt}\\Input') | ||
| else: | ||
| shell('copy "{new_file}" logs\\{dt}\\Input\\') | ||
| else: | ||
| shell("cp '{input_name}' logs/{dt}/input/") | ||
| shell("cp config.yaml logs/{dt}/") | ||
| shell("mkdir -p logs/{dt}/input/") | ||
| shell("cp '{log}' logs/{dt}/") | ||
| if os.path.isdir(input_name): | ||
| shell("cp '{input_name}'/*.* logs/{dt}/input/") | ||
| else: | ||
| shell("cp '{input_name}' logs/{dt}/input/") | ||
| shell("cp config.yaml logs/{dt}/") |
Contributor
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@standage I've added this to account for the different code required for a Mac/linux vs. windows os... is this kosher or not a good strategy to deal with it? This is the only difference between the Mac and windows version.
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Each of these shell commands has equivalents in pathlib. Let me see if I can replicate it...
from shutil import copy
input_name = Path(input_name)
dtdir = Path("logs") / dt
logdir = dtdir / "input"
logdir.mkdir(parents=True, exist_ok=True)
copy(log, logdir / log)
if input_name.is_dir():
for path in input_name.glob("*.*"):
copy(path, logdir / path.name)
else:
copy(input_name, logdir / input_name.name
copy("config.yaml", dtdir / "config.yaml")That should work cross-platform.
rnmitchell
commented
Jul 18, 2025
Comment on lines
-129
to
143
|
|
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| selected = option_menu( | ||
| menu_title=None, | ||
| options=["Home", "STRs", "SNPs", "How to Use", "Contact"], | ||
| icons=["house", "gear", "gear-fill", "book", "envelope"], | ||
| menu_icon="cast", | ||
| default_index=0, | ||
| orientation="horizontal", | ||
| ) | ||
| tab1, tab2, tab3, tab4, tab5 = st.tabs(["Home", "STRs", "SNPs", "How To Use", "Contact"]) | ||
|
|
||
| if selected == "Home": | ||
| with tab1: | ||
| show_home_page() | ||
|
|
||
| elif selected == "STRs": | ||
| with tab2: | ||
| show_STR_page() | ||
|
|
||
| elif selected == "SNPs": | ||
| with tab3: | ||
| show_SNP_page() | ||
|
|
||
| elif selected == "How to Use": | ||
| with tab4: | ||
| show_how_to_use_page() | ||
|
|
||
| elif selected == "Contact": | ||
| with tab5: | ||
| show_contact_page() |
Contributor
Author
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More changes to account for compatibility with Windows (the streamlit_option_menu package didn't work on Windows).
standage
requested changes
Jul 18, 2025
Member
standage
left a comment
standage
left a comment
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Looks ok overall, but I suggested a pure Python solution for copying the logs that should work across platforms.
Comment on lines
-129
to
143
|
|
||
| selected = option_menu( | ||
| menu_title=None, | ||
| options=["Home", "STRs", "SNPs", "How to Use", "Contact"], | ||
| icons=["house", "gear", "gear-fill", "book", "envelope"], | ||
| menu_icon="cast", | ||
| default_index=0, | ||
| orientation="horizontal", | ||
| ) | ||
| tab1, tab2, tab3, tab4, tab5 = st.tabs(["Home", "STRs", "SNPs", "How To Use", "Contact"]) | ||
|
|
||
| if selected == "Home": | ||
| with tab1: | ||
| show_home_page() | ||
|
|
||
| elif selected == "STRs": | ||
| with tab2: | ||
| show_STR_page() | ||
|
|
||
| elif selected == "SNPs": | ||
| with tab3: | ||
| show_SNP_page() | ||
|
|
||
| elif selected == "How to Use": | ||
| with tab4: | ||
| show_how_to_use_page() | ||
|
|
||
| elif selected == "Contact": | ||
| with tab5: | ||
| show_contact_page() |
Comment on lines
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| sample_df = np.where( | ||
| sample_df["Locus"] == "AMELOGENIN", | ||
| np.where(sample_df["CE_Allele"] == "X", 0, 1), | ||
| sample_df["CE_Allele"], | ||
| ) | ||
| #sample_df = np.where( | ||
| # sample_df["Locus"] == "AMELOGENIN", | ||
| # np.where(sample_df["CE_Allele"] == "X", "0.0", "1.0"), | ||
| # sample_df["CE_Allele"], | ||
| #) | ||
| for i, row in sample_df.iterrows(): | ||
| if row["Locus"] == "AMELOGENIN": | ||
| sample_df.loc[i, "CE_Allele"] = 0 if row.CE_Allele == "X" else 1 |
Member
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Let's figure out what to do with the commented out code before we merge.
lusSTR/workflows/strs.smk
Outdated
Comment on lines
77
to
94
| system = os.name | ||
| if system == "nt": | ||
| shell("md logs\\{dt}\\Input\\") | ||
| shell('copy "{log}" logs\\{dt}\\') | ||
| shell("copy config.yaml logs\\{dt}\\") | ||
| new_file = input_name.replace("/", "\\") | ||
| if os.path.isdir(input_name): | ||
| shell('xcopy "{new_file}" logs\\{dt}\\Input') | ||
| else: | ||
| shell('copy "{new_file}" logs\\{dt}\\Input\\') | ||
| else: | ||
| shell("cp '{input_name}' logs/{dt}/input/") | ||
| shell("cp config.yaml logs/{dt}/") | ||
| shell("mkdir -p logs/{dt}/input/") | ||
| shell("cp '{log}' logs/{dt}/") | ||
| if os.path.isdir(input_name): | ||
| shell("cp '{input_name}'/*.* logs/{dt}/input/") | ||
| else: | ||
| shell("cp '{input_name}' logs/{dt}/input/") | ||
| shell("cp config.yaml logs/{dt}/") |
Member
There was a problem hiding this comment.
Each of these shell commands has equivalents in pathlib. Let me see if I can replicate it...
from shutil import copy
input_name = Path(input_name)
dtdir = Path("logs") / dt
logdir = dtdir / "input"
logdir.mkdir(parents=True, exist_ok=True)
copy(log, logdir / log)
if input_name.is_dir():
for path in input_name.glob("*.*"):
copy(path, logdir / path.name)
else:
copy(input_name, logdir / input_name.name
copy("config.yaml", dtdir / "config.yaml")That should work cross-platform.
lusSTR/wrappers/filter.py
Outdated
Comment on lines
320
to
322
| # if df[df["SampleID"] == sample_id].empty: | ||
| # print(f"{sample_id} does not have any reads passing filter. Skipping to next sample.") | ||
| # else: |
standage
approved these changes
Jul 21, 2025
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Creating empty plots for samples with no reads above the detection threshold at any marker. This is to be able to evaluate negative samples (negative controls, RBs, etc.).