From 6adfed873713e8f9986d45eabeab787c0cb3791a Mon Sep 17 00:00:00 2001
From: Davide Albanese <davide.albanese@gmail.com>
Date: Thu, 10 Nov 2022 13:07:11 +0100
Subject: [PATCH] kofamscan: TSV output; fix merge_kofamscan_hits.py

---
 bin/merge_kofamscan_hits.py | 10 ++++++++--
 modules/kofamscan.nf        |  2 +-
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/bin/merge_kofamscan_hits.py b/bin/merge_kofamscan_hits.py
index 28c0d30..7c31dcf 100755
--- a/bin/merge_kofamscan_hits.py
+++ b/bin/merge_kofamscan_hits.py
@@ -17,8 +17,7 @@
 for input_fn in args.input:
     input_bn = os.path.basename(input_fn)
     input_id = input_bn.split(args.suffix)[0]
-    input_df = pd.read_fwf(input_fn, skiprows=[1],
-        colspecs = [(0, 1), (2, 22), (22, 29), (54, 1024)])
+    input_df = pd.read_csv(input_fn, delimiter='\t', skiprows=[1])
     input_df = input_df[input_df['#'] == '*']
     input_df = input_df.groupby(["KO", "KO definition"]) \
         [["gene name"]].nunique()
@@ -27,3 +26,10 @@
 
 compl_df.fillna(0, inplace=True)
 compl_df.to_csv('kofamscan_hits.tsv', sep='\t', float_format='%.d')
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diff --git a/modules/kofamscan.nf b/modules/kofamscan.nf
index 0946cb0..35d3d8e 100644
--- a/modules/kofamscan.nf
+++ b/modules/kofamscan.nf
@@ -15,7 +15,7 @@ process kofamscan {
     script:
     """
     exec_annotation \
-        -f detail \
+        -f detail-tsv \
         --cpu ${task.cpus} \
         --tmp-dir tmp \
         -o ${id}.hits.txt \