From 36a1cf180612a69508ff6652da05a0be80a688f7 Mon Sep 17 00:00:00 2001 From: Fengchao Date: Fri, 9 Mar 2018 09:44:25 +0800 Subject: [PATCH] Add ITAG data type. --- src/main/java/proteomics/TheoSeq/DbTool.java | 2 +- src/main/resources/parameter.def | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/proteomics/TheoSeq/DbTool.java b/src/main/java/proteomics/TheoSeq/DbTool.java index f43b4af..19e0ba0 100644 --- a/src/main/java/proteomics/TheoSeq/DbTool.java +++ b/src/main/java/proteomics/TheoSeq/DbTool.java @@ -26,7 +26,7 @@ public DbTool(String db_name, String databaseType) throws IOException { header_pattern = Pattern.compile("^>([^\\s]+)[\\s|]+(.+)$"); } else if (databaseType.contentEquals("UniProt") || databaseType.contentEquals("SwissProt")) { header_pattern = Pattern.compile("^>[^|]+\\|(.+)\\|(.+)$"); - } else if (databaseType.contentEquals("contaminants")) { + } else if (databaseType.contentEquals("contaminants") || databaseType.contentEquals("ITAG")) { header_pattern = Pattern.compile("^>([^ ]+) (.+)$"); } else if (databaseType.contentEquals("Others")) { header_pattern = Pattern.compile("^>(.+)$"); diff --git a/src/main/resources/parameter.def b/src/main/resources/parameter.def index 5d552c7..84df647 100644 --- a/src/main/resources/parameter.def +++ b/src/main/resources/parameter.def @@ -6,7 +6,7 @@ dev = 0 # Output development information. # Database db = small+random50.fasta # The protein database. -database_type = UniProt # Different types have different fasta header patterns. Available values: UniProt, SwissProt, TAIR, Others +database_type = UniProt # Different types have different fasta header patterns. Available values: UniProt, SwissProt, TAIR, ITAG, Others missed_cleavage = 2 # Maximum number of allowed missed cleavage. min_chain_length = 5 # Minimum length of a peptide chain. max_chain_length = 50