Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Update summarize_barrnap.py #716

Closed
wants to merge 1 commit into from
+5 −2
Closed

Update summarize_barrnap.py #716

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 5 additions & 2 deletions bin/summarize_barrnap.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,8 @@
# Takes a list of files with barrnap predictions (rrna.arc.gff, rrna.bac.gff, etc)
# for ASV sequences, extracts evalues for each prediction and summarize the results
# in a new file "summary.gff". Assumes that the same program/barrnap version is
# used for all predictions.
# used for all predictions. If there is more than one gene for a given domain,
# retains the lowest e-value (case of full rRNA operon sequences).

# import pandas as pd
import sys
Expand All @@ -27,7 +28,9 @@
method[asv] = rowparts[1]
if asv not in evalues:
evalues[asv] = dict()
evalues[asv][org] = rowparts[5]
if (org not in evalues[asv]) or (float(evalues[asv][org]) > float(rowparts[5])) :
evalues[asv][org] = rowparts[5]

fh.close()

# Write results
Expand Down
Loading