')
+ st.html(r'
')
col1,col2,col3 = st.columns([2,1,2])
From 94dff30c4ce45efbbeb0abb431db6ed74c9be5f5 Mon Sep 17 00:00:00 2001
From: Cameron Roots <38054423+croots@users.noreply.github.com>
Date: Fri, 16 May 2025 13:29:21 -0500
Subject: [PATCH 08/47] possible fix for download button
---
efmcalculator2/webapp/webapp.py | 54 ++++++++++++++-------------------
1 file changed, 22 insertions(+), 32 deletions(-)
diff --git a/efmcalculator2/webapp/webapp.py b/efmcalculator2/webapp/webapp.py
index c1f1497..d0b763f 100644
--- a/efmcalculator2/webapp/webapp.py
+++ b/efmcalculator2/webapp/webapp.py
@@ -39,39 +39,34 @@
import json
-
-
-def download_data(): # https://gist.github.com/snehankekre/2dcce9fb42b2f7e1742de7431326b263
- with TemporaryDirectory() as tempdir:
+@st.fragment
+def downloadfragment():
+ def download_data(tempdir): # https://gist.github.com/snehankekre/2dcce9fb42b2f7e1742de7431326b263
outputdir = tempdir + "/results"
os.mkdir(outputdir)
statemachine = st.session_state["statemachine"]
filetype = st.session_state["dlft"]
statemachine.save_results(outputdir, filetype=filetype)
- filestream=io.BytesIO() # https://stackoverflow.com/questions/75304410/streamlit-download-button-not-working-when-trying-to-download-files-as-zip
- with zipfile.ZipFile(filestream, mode='w', compression=zipfile.ZIP_DEFLATED) as zipf:
+ with zipfile.ZipFile(f"{outputdir}/results.zip", mode='w', compression=zipfile.ZIP_DEFLATED) as zipf:
for root, dirs, files in os.walk(outputdir):
for file in files:
zipf.write(os.path.join(root, file),
os.path.relpath(os.path.join(root, file),
os.path.join(outputdir, '..')))
- b64 = base64.b64encode(filestream.getvalue()).decode()
-
- dl_link = f"""
-
-
-
- 
-
- """,
- unsafe_allow_html=True
- )
+ col1,col2,col3 = st.columns([2,1,2])
+
+ with col1:
try:
from .._version import version_tuple
st.markdown(f"Version {version_tuple[0]}.{version_tuple[1]}.{version_tuple[2]} ([{str(version_tuple[4])[1:8]}](https://www.github.com/barricklab/efmcalculator2/commit/{str(version_tuple[4]).split('.')[0][1:8]}))")
except:
pass
- with colbadge:
st.html(r'
- EFM Calculator
-')
-
-
- col1,col2,col3 = st.columns([2,1,2])
-
- with col1:
upload_option = "Upload files (FASTA, GenBank, or CSV)"
enter_option = "Copy/Paste Plain Text"
example_option = "Example"
@@ -188,16 +174,11 @@ def run_webapp():
inSeq = None
- with col3:
- st.write("The EFM Calculator predicts mutational hotspots as a result of DNA polymerase slippage. It classifies these hotspots into three categories, Short Sequence Repeats, Short Repeated Sequences, and Repeat Mediated Deletions. For more information, please see the paper. If you have found this tool helpful, please remember to cite it as well.")
- st.write("Jack, B. R., Leonard, S. P., Mishler, D. M., Renda, B. A., Leon, D., Suárez, G. A., & Barrick, J. E. (2015). Predicting the Genetic Stability of Engineered DNA Sequences with the EFM Calculator. ACS Synthetic Biology, 4(8), 939–943. https://doi.org/10.1021/acssynbio.5b00068")
-
-
with TemporaryDirectory() as tempdir:
is_circular = True
field = None
if option == upload_option:
- with col1:
+ with col3:
is_circular = st.checkbox(label="Circular Prediction", value=True)
upload_disclaimer = f"Total sequence length must be less than {MAX_SIZE+1}. CSV files must have a 'seq' column and may have a 'name' column."
uploaded_files = st.file_uploader("Choose a file:", type=VALID_EXTS, accept_multiple_files = True)
@@ -233,25 +214,26 @@ def run_webapp():
elif option == enter_option:
with col1:
is_circular = st.checkbox(label="Circular Prediction", value=True)
- upload_disclaimer = f"""
-
"""
- field = st.text_area("Input sequence here:", max_chars=MAX_SIZE)
- st.markdown(upload_disclaimer, unsafe_allow_html=True)
- field = field.replace("\n", "")
- field = field.replace(" ", "")
- field = "".join([i for i in field if not i.isdigit()])
- last_text_input = st.session_state.get("last_text_input", "")
- if field:
- record = SeqRecord(Seq(field), id="sequence")
- originhash = hashlib.md5(("string" + field).encode())
- record = EFMSequence(record, is_circular, originhash)
- inSeq = [record]
- else:
- st.session_state["statemachine"] = StateMachine()
+ with col3:
+ upload_disclaimer = f"""Total sequence length must be less than {MAX_SIZE+1}.
-
+
"""
+ field = st.text_area("Input sequence here:", max_chars=MAX_SIZE)
+ st.markdown(upload_disclaimer, unsafe_allow_html=True)
+ field = field.replace("\n", "")
+ field = field.replace(" ", "")
+ field = "".join([i for i in field if not i.isdigit()])
+ last_text_input = st.session_state.get("last_text_input", "")
+ if field:
+ record = SeqRecord(Seq(field), id="sequence")
+ originhash = hashlib.md5(("string" + field).encode())
+ record = EFMSequence(record, is_circular, originhash)
+ inSeq = [record]
+ else:
+ st.session_state["statemachine"] = StateMachine()
elif option == example_option:
- with col1:
+ with col3:
gbs = []
examples_path = "examples/"
for infile_loc in glob.glob(os.path.join(examples_path, "*.gb")) + glob.glob(os.path.join(examples_path, "*.fasta")):
@@ -375,3 +357,6 @@ def run_webapp():
add_vertical_space(4)
seq_record.refreshed = False
+
+ st.write("The EFM Calculator predicts mutational hotspots as a result of DNA polymerase slippage. It classifies these hotspots into three categories, Short Sequence Repeats, Short Repeated Sequences, and Repeat Mediated Deletions. For more information, please see the paper. If you have found this tool helpful, please remember to cite it as well.")
+ st.write("Jack, B. R., Leonard, S. P., Mishler, D. M., Renda, B. A., Leon, D., Suárez, G. A., & Barrick, J. E. (2015). Predicting the Genetic Stability of Engineered DNA Sequences with the EFM Calculator. ACS Synthetic Biology, 4(8), 939–943. https://doi.org/10.1021/acssynbio.5b00068")
From cea1dfaa3f707009c3fc9005b319f932125e99d9 Mon Sep 17 00:00:00 2001
From: Cameron Roots <38054423+croots@users.noreply.github.com>
Date: Wed, 11 Jun 2025 11:18:34 -0700
Subject: [PATCH 30/47] Slightly better column sorting
---
efmcalculator2/webapp/webapp.py | 17 +++++++++--------
1 file changed, 9 insertions(+), 8 deletions(-)
diff --git a/efmcalculator2/webapp/webapp.py b/efmcalculator2/webapp/webapp.py
index cea3c7f..4f01920 100644
--- a/efmcalculator2/webapp/webapp.py
+++ b/efmcalculator2/webapp/webapp.py
@@ -155,13 +155,7 @@ def run_webapp():
statemachine = st.session_state["statemachine"]
col1,col2,col3 = st.columns([2,1,2])
-
with col1:
- try:
- from .._version import version_tuple
- st.markdown(f"Version {version_tuple[0]}.{version_tuple[1]}.{version_tuple[2]} ([{str(version_tuple[4])[1:8]}](https://www.github.com/barricklab/efmcalculator2/commit/{str(version_tuple[4]).split('.')[0][1:8]}))")
- except:
- pass
st.html(r'Total sequence length must be less than {MAX_SIZE+1}.
+')
upload_option = "Upload files (FASTA, GenBank, or CSV)"
enter_option = "Copy/Paste Plain Text"
@@ -174,14 +168,21 @@ def run_webapp():
inSeq = None
+ with col3:
+ try:
+ from .._version import version_tuple
+ st.markdown(f"Version {version_tuple[0]}.{version_tuple[1]}.{version_tuple[2]} ([{str(version_tuple[4])[1:8]}](https://www.github.com/barricklab/efmcalculator2/commit/{str(version_tuple[4]).split('.')[0][1:8]}))")
+ except:
+ pass
+
with TemporaryDirectory() as tempdir:
is_circular = True
field = None
if option == upload_option:
with col3:
is_circular = st.checkbox(label="Circular Prediction", value=True)
- upload_disclaimer = f"Total sequence length must be less than {MAX_SIZE+1}. CSV files must have a 'seq' column and may have a 'name' column."
- uploaded_files = st.file_uploader("Choose a file:", type=VALID_EXTS, accept_multiple_files = True)
+ upload_disclaimer = f"Total sequence length must be less than {MAX_SIZE+1}. CSV files must have a 'seq' column and may have a 'name' column."
+ uploaded_files = st.file_uploader("Choose a file:", type=VALID_EXTS, accept_multiple_files = True)
st.write(upload_disclaimer)
if uploaded_files:
inSeq = []
From 4a2464a74d97378217c4299dcbf846fb50991d9e Mon Sep 17 00:00:00 2001
From: Cameron Roots <38054423+croots@users.noreply.github.com>
Date: Wed, 11 Jun 2025 12:15:35 -0700
Subject: [PATCH 31/47] Remove badge, add back logo, push down right column
---
efmcalculator2/webapp/webapp.py | 16 +++++++++++++---
1 file changed, 13 insertions(+), 3 deletions(-)
diff --git a/efmcalculator2/webapp/webapp.py b/efmcalculator2/webapp/webapp.py
index 4f01920..0d96154 100644
--- a/efmcalculator2/webapp/webapp.py
+++ b/efmcalculator2/webapp/webapp.py
@@ -154,9 +154,17 @@ def run_webapp():
st.session_state["statemachine"] = StateMachine()
statemachine = st.session_state["statemachine"]
- col1,col2,col3 = st.columns([2,1,2])
+ col1,col2,col3 = st.columns([2,0.5,2])
with col1:
- st.html(r'')
+ st.markdown(
+ f"""
+
+
+
+ """,
+ unsafe_allow_html=True)
+
upload_option = "Upload files (FASTA, GenBank, or CSV)"
enter_option = "Copy/Paste Plain Text"
example_option = "Example"
@@ -169,6 +177,8 @@ def run_webapp():
inSeq = None
with col3:
+ st.text("")
+ st.text("")
try:
from .._version import version_tuple
st.markdown(f"Version {version_tuple[0]}.{version_tuple[1]}.{version_tuple[2]} ([{str(version_tuple[4])[1:8]}](https://www.github.com/barricklab/efmcalculator2/commit/{str(version_tuple[4]).split('.')[0][1:8]}))")
@@ -271,7 +281,7 @@ def run_webapp():
else:
disable_dropdown = False
- col4,col5,col6 = st.columns([2,1,2])
+ col4,col5,col6 = st.columns([2,0.5,2])
with col4:
selected_sequence = st.selectbox(
From 5afc53d23e46fe2fac3c280629a4c74447e8f699 Mon Sep 17 00:00:00 2001
From: Cameron Roots <38054423+croots@users.noreply.github.com>
Date: Wed, 11 Jun 2025 12:28:21 -0700
Subject: [PATCH 32/47] Uncolumn the input layout.
---
efmcalculator2/webapp/webapp.py | 33 ++++++++++++++++-----------------
1 file changed, 16 insertions(+), 17 deletions(-)
diff --git a/efmcalculator2/webapp/webapp.py b/efmcalculator2/webapp/webapp.py
index 0d96154..c6e4ee8 100644
--- a/efmcalculator2/webapp/webapp.py
+++ b/efmcalculator2/webapp/webapp.py
@@ -225,23 +225,22 @@ def run_webapp():
elif option == enter_option:
with col1:
is_circular = st.checkbox(label="Circular Prediction", value=True)
- with col3:
- upload_disclaimer = f"""
+ EFM Calculator
+
-
"""
- field = st.text_area("Input sequence here:", max_chars=MAX_SIZE)
- st.markdown(upload_disclaimer, unsafe_allow_html=True)
- field = field.replace("\n", "")
- field = field.replace(" ", "")
- field = "".join([i for i in field if not i.isdigit()])
- last_text_input = st.session_state.get("last_text_input", "")
- if field:
- record = SeqRecord(Seq(field), id="sequence")
- originhash = hashlib.md5(("string" + field).encode())
- record = EFMSequence(record, is_circular, originhash)
- inSeq = [record]
- else:
- st.session_state["statemachine"] = StateMachine()
+ upload_disclaimer = f"""Total sequence length must be less than {MAX_SIZE+1}.
-
+
"""
+ field = st.text_area("Input sequence here:", max_chars=MAX_SIZE)
+ st.markdown(upload_disclaimer, unsafe_allow_html=True)
+ field = field.replace("\n", "")
+ field = field.replace(" ", "")
+ field = "".join([i for i in field if not i.isdigit()])
+ last_text_input = st.session_state.get("last_text_input", "")
+ if field:
+ record = SeqRecord(Seq(field), id="sequence")
+ originhash = hashlib.md5(("string" + field).encode())
+ record = EFMSequence(record, is_circular, originhash)
+ inSeq = [record]
+ else:
+ st.session_state["statemachine"] = StateMachine()
elif option == example_option:
with col3:
From 0d621956ea4eee7145b4854562c6bf80b3f6f187 Mon Sep 17 00:00:00 2001
From: kevin99111 Total sequence length must be less than {MAX_SIZE+1}.
+