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Merge pull request #71 from Jumitti/beta
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Beta
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@Jumitti
Jumitti authored Oct 18, 2024
2 parents 8b2759b + 94e8f64 commit 011c075
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Showing 2 changed files with 74 additions and 72 deletions.
47 changes: 36 additions & 11 deletions navigation/aio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,8 @@ def result_table_output(df):
y=alt.Y('Rel Score:Q', axis=alt.Axis(title='Relative Score'),
scale=alt.Scale(domain=[ystart, ystop])),
color=alt.condition(gene_region_selection, color_scale, alt.value('lightgray')),
tooltip=['Sequence', 'Position'] + (['Rel Position'] if "Rel Position" in source else []) + ['Rel Score'] + (
tooltip=['Sequence', 'Position'] + (['Rel Position'] if "Rel Position" in source else []) + (
['Ch Position'] if "Ch Position" in source else []) + ['Rel Score'] + (
['p-value'] if 'p-value' in source else []) + ['Gene', 'Species', 'Region'],
opacity=alt.condition(gene_region_selection, alt.value(0.8), alt.value(0.2))
).transform_calculate(x=f'datum[{xcol_param.name}]').properties(width=600,
Expand Down Expand Up @@ -178,7 +179,8 @@ def aio_page():
# Species
st.markdown("🔹 :blue[**Step 1.2**] Species of gene names and sliced variants:")
col1, col2, col3 = st.columns(3)
gr = col1.selectbox("Genome:", ["Current", "Previous"], index=0, help='Example for Homo sapiens:\n\n"Current" is GRCh38\n\n"Previous" is GRCh37')
gr = col1.selectbox("Genome:", ["Current", "Previous"], index=0,
help='Example for Homo sapiens:\n\n"Current" is GRCh38\n\n"Previous" is GRCh37')
species = col2.selectbox("Species:", ["Human", "Mouse", "Rat", "Drosophila", "Zebrafish"], index=0)
col3.markdown("")
col3.markdown("")
Expand Down Expand Up @@ -227,7 +229,8 @@ def aio_page():
pbar.progress(i / len(gene_ids),
text=f'**:blue[Extract sequence... {gene_id}] ⚠️:red[PLEASE WAIT UNTIL END WITHOUT CHANGING ANYTHING]**')
result_promoter_output, message = NCBIdna(gene_id, prom_term, upstream, downstream,
species, gr, all_slice_forms=True if all_variants else False).find_sequences()
species, gr,
all_slice_forms=True if all_variants else False).find_sequences()
if message == "OK":
pbar.progress((i + 1) / len(gene_ids),

Expand Down Expand Up @@ -458,7 +461,9 @@ def aio_page():
name = "n.d."
species = "n.d"
region = "n.d"
dna_sequences.append((name, dna_sequence, species, region))
strand = "n.d"
tss_ch = 0
dna_sequences.append((name, dna_sequence, species, region, strand, tss_ch))
elif lines.startswith(">"):
lines = dna_sequence.split("\n")
i = 0
Expand Down Expand Up @@ -490,7 +495,22 @@ def aio_page():
region = "n.d"
dna_sequence = lines[i + 1].upper()
isfasta = IMO.is_dna(dna_sequence)
dna_sequences.append((name, dna_sequence, found_species, region))

match = re.search(r"Strand:\s*(\w+)", line)
if match:
strand = match.group(1).lower()
if strand not in ["plus", "minus"]:
strand = "n.d"
else:
strand = "n.d"

match = re.search(r"TSS \(on chromosome\):\s*(\d+)", line)
if match:
tss_ch = match.group(1)
else:
tss_ch = 0

dna_sequences.append((name, dna_sequence, found_species, region, strand, tss_ch))
i += 1
else:
i += 1
Expand All @@ -499,7 +519,7 @@ def aio_page():
else:
isfasta = False

total_sequences_region_length = sum(len(dna_sequence) for _, dna_sequence, _, _ in dna_sequences)
total_sequences_region_length = sum(len(dna_sequence) for _, dna_sequence, _, _, _, _ in dna_sequences)
total_sequences = len(dna_sequences)

# RE entry
Expand Down Expand Up @@ -546,7 +566,8 @@ def aio_page():
help="Only PWM generated with our tools are allowed")
matrix_str = st.text_area("🔹 :blue[**Step 2.3**] Matrix:",
value="A [ 20.0 0.0 0.0 0.0 0.0 0.0 0.0 100.0 0.0 60.0 20.0 ]\nT [ 60.0 20.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 ]\nG [ 0.0 20.0 100.0 0.0 0.0 100.0 100.0 0.0 100.0 40.0 0.0 ]\nC [ 20.0 60.0 0.0 100.0 100.0 0.0 0.0 0.0 0.0 0.0 80.0 ]"
if 'MATRIX_STR_save' not in st.session_state else st.session_state['MATRIX_STR_save'],
if 'MATRIX_STR_save' not in st.session_state else st.session_state[
'MATRIX_STR_save'],
label_visibility='collapsed', height=125)
st.session_state['MATRIX_STR_save'] = matrix_str

Expand Down Expand Up @@ -582,7 +603,8 @@ def aio_page():
help='Put FASTA sequences. Same sequence length required ⚠')
individual_motif = st.text_area("🔹 :blue[**Step 2.3**] Sequences:",
value=">seq1\nCTGCCGGAGGA\n>seq2\nAGGCCGGAGGC\n>seq3\nTCGCCGGAGAC\n>seq4\nCCGCCGGAGCG\n>seq5\nAGGCCGGATCG"
if 'individual_motif_save' not in st.session_state else st.session_state['individual_motif_save'],
if 'individual_motif_save' not in st.session_state else
st.session_state['individual_motif_save'],
label_visibility='collapsed')
st.session_state['individual_motif_save'] = individual_motif
individual_motif = individual_motif.upper()
Expand Down Expand Up @@ -707,8 +729,9 @@ def aio_page():
calc_pvalue = None

with BSFcol3:
st.markdown("🔹 :blue[**_Experimental_**] Analyse all directions", help='Directions: **original (+ →)**, **reverse-complement (- ←)**, reverse (+ ←), complement (- →)\n\n'
'Directions in bold are the default directions.')
st.markdown("🔹 :blue[**_Experimental_**] Analyse all directions",
help='Directions: **original (+ →)**, **reverse-complement (- ←)**, reverse (+ ←), complement (- →)\n\n'
'Directions in bold are the default directions.')
alldirection = st.toggle('All directions')
if alldirection:
st.markdown(
Expand Down Expand Up @@ -754,7 +777,6 @@ def aio_page():
if st.button("🔹 :blue[**Step 2.6**] Click here to find motif in your sequences 🔎 🧬",
use_container_width=True,
disabled=button):

motif = motifs.Motif(counts=matrix)
pwm = motif.counts.normalize(pseudocounts=0.1)
log_odds_matrix = pwm.log_odds()
Expand All @@ -776,6 +798,9 @@ def aio_page():

df = pd.DataFrame(st.session_state['individual_motif_occurrences'][1:],
columns=st.session_state['individual_motif_occurrences'][0])

df = df.sort_values(by='Rel Score', ascending=False)

st.session_state['df'] = df

st.markdown('**Table**')
Expand Down
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