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.. _extract_seqs_by_sample_id:
.. index:: extract_seqs_by_sample_id.py
*extract_seqs_by_sample_id.py* -- Extract sequences based on the SampleID
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
**Description:**
This script creates a fasta file which will contain only sequences that ARE associated with a set of sample IDs, OR all sequences that are NOT associated with a set of sample IDs (-n)
**Usage:** :file:`extract_seqs_by_sample_id.py [options]`
**Input Arguments:**
.. note::
**[REQUIRED]**
-i, `-`-input_fasta_fp
Path to the input fasta file
-o, `-`-output_fasta_fp
The output fasta file
**[OPTIONAL]**
-n, `-`-negate
Negate the sample ID list (i.e., output sample ids not passed via -s) [default: False]
-s, `-`-sample_ids
Comma-separated sample_ids to include in output fasta file (or exclude if --negate), or string describing mapping file states defining sample ids (mapping_fp must be provided for the latter)
-m, `-`-mapping_fp
The mapping filepath
**Output:**
The script produces a fasta file containing containing only the specified SampleIDs.
**Examples:**
Create the file outseqs.fasta (-o), which will be a subset of inseqs.fasta (-i) containing only the sequences THAT ARE associated with sample ids S2, S3, S4 (-s). As always, sample IDs are case-sensitive:
::
extract_seqs_by_sample_id.py -i inseqs.fasta -o outseqs_by_sample.fasta -s S2,S3,S4
Create the file outseqs.fasta (-o), which will be a subset of inseqs.fasta (-i) containing only the sequences THAT ARE NOT (-n) associated with sample ids S2, S3, S4 (-s). As always, sample IDs are case-sensitive:
::
extract_seqs_by_sample_id.py -i inseqs.fasta -o outseqs_by_sample_negated.fasta -s S2,S3,S4 -n
Create the file outseqs.fasta (-o), which will be a subset of inseqs.fasta (-i) containing only the sequences THAT ARE associated with sample ids whose "Treatment" value is "Fast" in the mapping file:
::
extract_seqs_by_sample_id.py -i inseqs.fasta -o outseqs_by_mapping_field.fasta -m map.txt -s "Treatment:Fast"
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