From 7ed8138e7da5ee5443e4cdc16eda08ea5c1508a4 Mon Sep 17 00:00:00 2001 From: Nicolae Sapoval Date: Mon, 11 Mar 2024 21:22:21 -0500 Subject: [PATCH 1/3] Not storign CIGARs for minimap2 AS mode --- lemur.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/lemur.py b/lemur.py index d7ff8f2..a183ecb 100644 --- a/lemur.py +++ b/lemur.py @@ -386,7 +386,8 @@ def build_P_rgs_df(self): P_rgs_data["Read_ID"].append(qname) P_rgs_data["Target_ID"].append(species_tid) - P_rgs_data["cigar"].append(cigar) + if not self.args.minimap2_AS: + P_rgs_data["cigar"].append(cigar) P_rgs_data["Gene"].append(gene) P_rgs_data["Reference"].append(aln.reference_name) P_rgs_data["aln_len"].append(self.__get_aln_len(aln)) @@ -423,6 +424,7 @@ def build_P_rgs_df(self): repeat(self.fixed_cigar))) del P_rgs_data["cigar"] + self.P_rgs_df = pd.DataFrame(data=P_rgs_data) self.P_rgs_df["max_aln_len"] = self.P_rgs_df.groupby("Read_ID")["aln_len"].transform('max') self.P_rgs_df["log_P"] = self.P_rgs_df["log_P"] * self.P_rgs_df["max_aln_len"] / self.P_rgs_df["aln_len"] From a6f3c8ee537356feccd2c5496b4252fc3b9e86b3 Mon Sep 17 00:00:00 2001 From: Bryce Lorenz Kille Date: Mon, 25 Mar 2024 10:20:25 -0500 Subject: [PATCH 2/3] Update minimap2_AS flag to current CLI flags --- lemur | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lemur b/lemur index a36937f..22bc41d 100755 --- a/lemur +++ b/lemur @@ -422,7 +422,7 @@ class LemurRunEnv(): P_rgs_data["Read_ID"].append(qname) P_rgs_data["Target_ID"].append(species_tid) - if not self.args.minimap2_AS: + if not self.args.aln_score == "AS": P_rgs_data["cigar"].append(cigar) P_rgs_data["Gene"].append(gene) P_rgs_data["Reference"].append(aln.reference_name) From 2d70adfe595d2ad0999ac8230ccdca40e5394fdb Mon Sep 17 00:00:00 2001 From: Bryce Lorenz Kille Date: Mon, 25 Mar 2024 10:22:07 -0500 Subject: [PATCH 3/3] Update version --- lemur | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lemur b/lemur index 22bc41d..ea20741 100755 --- a/lemur +++ b/lemur @@ -19,7 +19,7 @@ import numpy as np import pysam -__version__ = "1.0.0" +__version__ = "1.0.1" def CTRLChandler(signum, frame):