BBMap Converter

• pt-br

Mapping Converter is a module from the project TaxAM created to convert Mapping file generated by the Software BBMap:

It will turn the file in the format:

@HD	VN:1.4	SO:unsorted
@SQ	SN:NC_004718.3	LN:29751
@SQ	SN:NC_009452.1	LN:23814
@SQ	SN:NC_014373.1	LN:18940
@SQ	SN:NC_043439.1	LN:11916
@SQ	SN:NC_055325.1	LN:6406
@SQ	SN:NC_055508.1	LN:15270
@PG	ID:BBMap	PN:BBMap	VN:38.94	CL:java -ea -Xmx1871m -Xms1871m align2.BBMap build=1 overwrite=true fastareadlen=500 in=/data/viruses_data_01/final_sg.fa out=/data/viruses_data_01/mapping_01.txt ref=/data/viruses_data_01/contigs.fa
read_201	0	NC_014373.1	9665	43	75=	*	0	0	TTAATCACTTATATTGTATTCATTTGAAATTACTCATTAGGCAAATACTTTGATTAAGAAAAAATAATTGGAAAA	*	NM:i:0	AM:i:43
read_202	16	NC_009452.1	19020	43	75=	*	0	0	ACTGGTTAGTATTAGATGCTATCCTACACACTAGATCATTCATAGAAGCAATTGATTTCCTAGTTAACAATCCAC	*	NM:i:0	AM:i:43
read_203	0	NC_055325.1	2562	43	75=	*	0	0	CCTTGAGAGATTGGCGACATTAAAGGCCACAAGTAACTTCAATAATGGATGGTATAACTATAAGGAAGTAAAAGA	*	NM:i:0	AM:i:43
read_204	16	NC_014373.1	2079	43	75=	*	0	0	TGCCACAAGTACAGGACAGATCCGAAAATCATGACCAAACCCTTCAAACACAGTCCAGGGTTTTGACTCCTATCA	*	NM:i:0	AM:i:43
read_205	0	NC_004718.3	26316	43	75=	*	0	0	CTTCTGAAGGAGTTCCTGATCTTCTGGTCTAAACGAACTAACTATTATTATTATTCTGTTTGGAACTTTAACATT	*	NM:i:0	AM:i:43

into a :

read_201    NC_014373.1
read_202    NC_009452.1
read_203    NC_055325.1
read_204    NC_014373.1
read_205    NC_004718.3

Use example:

python mappingConverter -mp "/samples/bbmap/" -op "fileCoverted"

Parsers:

• -mp : Folder where are the files to be converted.
• -op : Nome dos arquivos finais. Se essa flag não for informada, o programa irá usar os nomes dos arquivos originais para criar esses nomes.
• -op : Final files name. If this flag is not informed, the program will use the original file names to create these names.
• -ms : Separator used between each item of each line to be converted.
• -os : Separador usado entre os itens de cada linha dos arquivos convertidos.
• -os : Separator used between each item of each line to be converted.

The converted files will be stored in a folder called /output_converter/ inside the folder /mappingConverter/.