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<< Back | Workflows ::: Manipulate genomic sequences

3.3 - Select regions of interest

HaploMake can be used to extract specific parts of a genomic sequence and its annotation by providing a single region.

Example

To extract the reverse complement of a region on chromosome 4 (chr04), from 1,500,000~2,000,000 bp, run:

export HaploSync_path="/path/to/HaploSync"
${HaploSync_path}/HaploMake.py -f genome.fasta -g annotation.gff3 -s region.file --format ${region.file_format} --skipoverlap

with

  • -f genome.fasta: Genomic sequences.

  • -g annotation.gff3: Genomic annotation.

  • -p | —prefix: Control the output sequence ID.

  • -s region.file and --format ${region.file_format}: The region to extract and the format of input. The structure can be in any of the following formats:

    • BED:

      chr04	1499999	2000000	.	.	-
      • Use bed6 format to include the orientation of the region to extract. Otherwise, it will be assumed to be the same as the reference sequences (+).
      • Different regions can be extracted at the same time by submitting a comma-separated list of bed files.
      • Starting coordinate is 0-based.
      • BED file format specifications.

    • AGP:

      New_seq	1	500000	1	W	chr04	1500000	2000000	-
      • The file names a new sequence,New_seq, that is 500Kb long, and corresponds to the region to extract.
      • Output sequence ID can be controlled from the AGP file and/or by using the -p | —prefix flag.
      • Different regions can be extracted by including them on different lines and different output sequence IDs (like New_seq1, New_seq2, etc.) and/or submitting a comma-separated list of files.
      • Starting coordinate is 1-based.

    • AGP file format.

    • BLOCK:

      >New_seq
chr04	1499999	2000000	-
      • The file names a new sequence, New_seq, made from the selected region.
      • Output sequence ID can be controlled from the BLOCK file and/or by using the -p | —prefix flag.
      • Multiple regions can be extracted at the same time by listing different blocks with different output sequence IDs (like New_seq1, New_seq2, etc.) in the BLOCK file and/or by submitting a comma-separated list of files.
      • Starting coordinate is 0-based.
      • BLOCK file format.

See HaploMake usage page for a complete description of usage options.

Output

  • out.fasta: FASTA of the selected sequence region with the new given name (New_seq).
  • out.gff3: Annotation of the selected region with coordinates translated to the new sequence (New_seq based).
  • out.agp: AGP file associating the selected region to the output. See the AGP file format specifications for a complete description of its format.
    • If the input is in AGP format (region.agp), the two files are identical.