From a87e2cd7cb3731070951b9b7403836c27165c482 Mon Sep 17 00:00:00 2001 From: Dominik R Laetsch Date: Wed, 26 Jul 2017 08:39:06 +0100 Subject: [PATCH] Fix - generate_kinfin_input.py now technically also can deal with multiline FASTAs --- scripts/generate_kinfin_input.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/scripts/generate_kinfin_input.py b/scripts/generate_kinfin_input.py index bc64538..c55a22c 100755 --- a/scripts/generate_kinfin_input.py +++ b/scripts/generate_kinfin_input.py @@ -76,13 +76,13 @@ def parse_fasta_dir(self): def parse_fasta_f(self, fasta_f, species_idx): seq_count = 0 - for seq_idx, line in enumerate(read_file(fasta_f)): + for line in read_file(fasta_f): if line and line[0] == '>': - seq_count += 1 header = line[1:].split()[0] if self.orthofinder_flag: header = header.replace(":", "_").replace(",", "_").replace("(", "_").replace(")", "_") - self.sequence_id_lines.append("%s_%s: %s" % (species_idx, seq_idx, header)) + self.sequence_id_lines.append("%s_%s: %s" % (species_idx, seq_count, header)) + seq_count += 1 print "[+] \t %s sequences parsed" % (seq_count) def write_files(self):