Skip to content

Commit

Permalink
added -i option to ignore header formats. to be used with -v for sing…
Browse files Browse the repository at this point in the history 
…le genomes per file
  • Loading branch information
Shinichi Sunagawa committed Apr 4, 2020
1 parent 322940a commit 5342fa4
Show file tree
Hide file tree
Showing 2 changed files with 40 additions and 22 deletions.
37 changes: 23 additions & 14 deletions README.txt
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@

===============
fetchMGs v 1.1
fetchMGs v 1.2
===============


Expand Down Expand Up @@ -82,19 +82,28 @@ Usage
fetchMGs.pl -m|mode <extraction|calibration> [OPTIONS]

Extraction mode
./fetchMGs.pl -m extraction <protein sequences> [optional options]
<protein sequences> Multi-FASTA file with protein sequences from which marker genes should be extracted
-c|og_used Orthologous group id to be extracted; example: 'COG0012'; default = 'all'
-o|outdir Output directory; default = 'output'
-h|hmmdir Path to directory that contains hmm models; default = './lib'
-b|bitscore Path to bitscore cutoff file; default = 'lib/MG_BitScoreCutoffs.defaults.txt'
-p|protein_only Set if nucleotide sequences for filename.faa is not available
-v|verybesthit_only Recommended to use, if extracting sequences from reference genomes.
For this fasta identifiers should be in the form: taxID.geneID and,
if needed have ' project_id=XXX' somewhere in the header
-t|threads Number of processors/threads to be used
-d|dnaFastaFile Fasta file with DNA sequences of the same genes; not neccesary if protein file and dna file have the same with .faa and .fna suffixes
-x|xbin Path to binaries used by this script. default = '' --> will search for variables in $PATH
./fetchMGs.pl [options] -m extraction <protein sequences>
<protein sequences> Multi-FASTA file with protein sequences from which universal single-copy marker genes should be extracted
-c|og_used Orthologous group id to be extracted; example: \'COG0012\'; default = \'all\'
-o|outdir Output directory; default = \'output\'
-b|bitscore Path to bitscore cutoff file;
Default = \'\$pathInWhichThisScriptResides/lib/MG_BitScoreCutoffs.[allhits|verybesthit].txt\' (depending on -v option)
-l|library Path to directory that contains hmm models;
default = \'\$pathInWhichThisScriptResides/lib\'
-p|protein_only Set if nucleotide sequences file for <protein sequences> is not available
-d|dnaFastaFile Multi-FASTA file with nucleotide sequences file for <protein sequences>;
not neccesary if protein and nucleotide fasta file have the same name except .faa and .fna suffixes
-v|verybesthit_only Only extract the best hit of each OG from each genome.
Recommended to use, if extracting sequences from multiple reference genomes in the same file.
Do not use it for metagenomes.
If this option is set fasta identifiers should be in the form: taxID.geneID and, if needed, have 'project_id=XXX' in the header.
Alternatively, set -i to ignore the headers. Then, the best hit of each OG in the whole input file will be selected, regardless of the headers used.
-i|ignore_headers If this option is set in addition to -v, the best hit of each COG will be selected.
Recommended to use, if extracting sequences from a single genome in the same file.
-t|threads Number of processors/threads to be used
-x|executables Path to executables used by this script (hmmsearch; seqtk).
default = \'\$pathInWhichThisScriptResides/bin\'
If set to \'\' will search for executables in \$PATH

Calibration mode
./fetchMGs.pl -m calibration <reference protein sequences> <true positives map>
Expand Down
25 changes: 17 additions & 8 deletions fetchMGs.pl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,6 +22,7 @@
Extraction mode
./fetchMGs.pl [options] -m extraction <protein sequences>
<protein sequences> Multi-FASTA file with protein sequences from which universal single-copy marker genes should be extracted
-c|og_used Orthologous group id to be extracted; example: \'COG0012\'; default = \'all\'
-o|outdir Output directory; default = \'output\'
-b|bitscore Path to bitscore cutoff file;
default = \'\$pathInWhichThisScriptResides/lib/MG_BitScoreCutoffs.[allhits|verybesthit].txt\' (depending on -v option)
Expand All @@ -30,12 +31,13 @@
-p|protein_only Set if nucleotide sequences file for <protein sequences> is not available
-d|dnaFastaFile Multi-FASTA file with nucleotide sequences file for <protein sequences>;
not neccesary if protein and nucleotide fasta file have the same name except .faa and .fna suffixes
-v|verybesthit_only Only extract the best hit to each OG from each genome.
Recommended to use, if extracting sequences from reference genomes.
Please do not use for metagenomes.
If this option is set fasta identifiers should be in the form: taxID.geneID and,
if needed have \' project_id=XXX\' somewhere in the header
-c|og_used Orthologous group id to be extracted; example: \'COG0012\'; default = \'all\'
-v|verybesthit_only Only extract the best hit of each OG from each genome.
Recommended to use, if extracting sequences from multiple reference genomes in the same file.
Do not use it for metagenomes.
If this option is set fasta identifiers should be in the form: taxID.geneID and, if needed, have 'project_id=XXX' in the header.
Alternatively, set -i to ignore the headers. Then, the best hit of each OG in the whole input file will be selected, regardless of the headers used.
-i|ignore_headers If this option is set in addition to -v, the best hit of each COG will be selected.
Recommended to use, if extracting sequences from a single genome in the same file.
-t|threads Number of processors/threads to be used
-x|executables Path to executables used by this script (hmmsearch; seqtk).
default = \'\$pathInWhichThisScriptResides/bin\'
Expand Down Expand Up @@ -65,6 +67,7 @@
my $cutoff_file = "DEFAULT";
my $protein_only = 0;
my $besthit_only = 0;
my $ignoreheaders = 0;
my $intProcessorNumber = 1;
my $floatMin = 60;
my $manual = 0;
Expand Down Expand Up @@ -92,6 +95,7 @@
'b|bitscore=s' => \$cutoff_file,
'p|protein_only' => \$protein_only,
'v|verybesthit_only' => \$besthit_only,
'i|ignore_headers' => \$ignoreheaders,
't|threads=i' => \$intProcessorNumber,
'd|dnaFastaFile=s' => \$strDNAFastaFileName,
'x|executables=s' => \$bin
Expand Down Expand Up @@ -206,7 +210,7 @@

print "
===================================================================================
FetchMGs v1.1 - extraction of marker genes from protein sequences
FetchMGs v1.2 - extraction of marker genes from protein sequences
Copyright (c) 2019 Shinichi Sunagawa, Daniel R Mende
===================================================================================
Expand Down Expand Up @@ -473,7 +477,12 @@ sub filterResultsArray_besthitAmongGenomes {
for my $i ( 0 .. $#arrAllResults ) {

my $strQueryId = $arrAllResults[$i][0];
my $strTaxProjectID = $arrAllResults[$i][1];
# EDIT
my $strTaxProjectID;
if ( $ignoreheaders ) {
$strTaxProjectID = "X" }else{
$strTaxProjectID = $arrAllResults[$i][1];
}
my $strCOGid = $arrAllResults[$i][2];
my $floatBitscore = $arrAllResults[$i][3];

Expand Down

0 comments on commit 5342fa4

Please sign in to comment.