-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Add tool.hatch.build.targets to pyproject.toml
- v0.22.3
- v0.22.2
- v0.22.1
- v0.22.0
- v0.21.1
- v0.21.0
- v0.20.1
- v0.20.0
- v0.19.2
- v0.19.1
- v0.19.0
- v0.18.2
- v0.18.1
- v0.18.0
- v0.17.6
- v0.17.5
- v0.17.4
- v0.17.3
- v0.17.2
- v0.17.1
- v0.17.0
- v0.16.5
- v0.16.4
- v0.16.3
- v0.16.2
- v0.16.1
- v0.16.0
- v0.15.6
- v0.15.5
- v0.15.4
- v0.15.3
- v0.15.2
- v0.15.1
- v0.15.0
- v0.14.1
- v0.14.0
- v0.13.1
- v0.13.0
- v0.12.2
- v0.12.1
- v0.12.0
- v0.11.5
- v0.11.4
- v0.11.3
- v0.11.2
- v0.11.1
- v0.11.0
- v0.10.0
- v0.9.8
- v0.9.7
- v0.9.6
- v0.9.5
- v0.9.4
- v0.9.3
- v0.9.2
- v0.9.1
- v0.9.0
- v0.8.0
- v0.7.1
1 parent
b5615da
commit ddaff9c
Showing
10 changed files
with
136 additions
and
235 deletions.
There are no files selected for viewing
This file was deleted.
Oops, something went wrong.
Binary file not shown.
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
File renamed without changes
File renamed without changes.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,70 @@ | ||
|
||
Input file patterns | ||
======================================================================== | ||
|
||
For commands that take a list of input files as positional arguments, | ||
these files can be given in a variety of ways so that you can choose a | ||
convenient manner of specifying input files. | ||
|
||
Example output directory | ||
------------------------------------------------------------------------ | ||
|
||
Assume that the output directory has these contents:: | ||
|
||
sample_1/ | ||
align/ | ||
ref_1.bam | ||
ref_2.bam | ||
relate/ | ||
ref_1/ | ||
batch-relate-0.parquet | ||
report-relate.json | ||
ref_2/ | ||
batch-relate-0.parquet | ||
report-relate.json | ||
mask/ | ||
ref_1/ | ||
batch-mask-0.csv.gz | ||
report-mask.json | ||
ref_2/ | ||
batch-mask-0.csv.gz | ||
report-mask.json | ||
sample_2/ | ||
align/ | ||
ref_1.bam | ||
ref_2.bam | ||
relate/ | ||
ref_1/ | ||
batch-relate-0.parquet | ||
report-relate.json | ||
ref_2/ | ||
batch-relate-0.parquet | ||
report-relate.json | ||
mask/ | ||
ref_1/ | ||
batch-mask-0.csv.gz | ||
report-mask.json | ||
ref_2/ | ||
batch-mask-0.csv.gz | ||
report-mask.json | ||
|
||
List of files | ||
------------------------------------------------------------------------ | ||
|
||
The simplest manner is to list every input file explicitly. For example, | ||
two report files could be processed with ``table`` command like this:: | ||
|
||
seismic table sample_1/relate/ref_1/report-relate.json sample_2/mask/ref_2/report-relate.json | ||
|
||
Glob patterns | ||
------------------------------------------------------------------------ | ||
|
||
Listing many input files explicitly would be tedious. `Glob patterns`_ | ||
use wildcard characters to match many paths with a single expression. | ||
This method is especially useful for matching files that have the same | ||
names and are located in different directories. For example, to process | ||
all report files for the reference ``ref_2``:: | ||
|
||
|
||
.. _glob patterns: https://en.wikipedia.org/wiki/Glob_(programming) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,53 @@ | ||
|
||
Relate each read to every reference position | ||
------------------------------------------------------------------------ | ||
|
||
Input files for relate | ||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ | ||
|
||
Relate requires exactly one FASTA file containing one or more reference | ||
sequences and any number of alignment map files in BAM format. | ||
|
||
.. note:: | ||
The references in the FASTA file must match those to which the reads | ||
were aligned to produce the BAM file(s); the names and the sequences | ||
must be identical. If the names differ, then the BAM files using the | ||
old names will be ignored; while if the sequences differ, then reads | ||
can yield erroneous relation vectors or fail outright. | ||
|
||
One BAM file | ||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" | ||
|
||
A single BAM file (``sample_1/align/ref_1.bam``) can be run as follows:: | ||
|
||
seismic relate refs.fa sample_1/align/ref_1.bam | ||
|
||
Multiple BAM files | ||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" | ||
|
||
Multiple BAM files can be run in parallel by giving multiple paths:: | ||
|
||
seismic relate refs.fa sample_1/align/ref_1.bam | ||
|
||
and/or by using `glob patterns`_:: | ||
|
||
seismic relate refs.fa sample_*/align/ref_1.bam sample_*/align/ref_2.bam | ||
|
||
BAM file content conventions | ||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" | ||
|
||
Generally, a BAM file can contain reads that have aligned to any number | ||
of reference, as well as unaligned reads. However, SEISMIC-RNA requires | ||
that each BAM file contain reads aligned to exactly one reference. This | ||
restriction enables the relate step to process BAM files in parallel, | ||
which increases the speed. If the BAM files were created using ``seismic | ||
align``, then they will already follow this convention. | ||
|
||
BAM file path conventions | ||
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" | ||
|
||
The name of the BAM file (minus the extension ``.bam``) must be the name | ||
of the reference to which it was aligned. It must be inside a directory | ||
named ``align``, which must be inside a directory named after the sample | ||
from which the reads came. If the BAM files were created using ``seismic | ||
align``, then they will already follow this convention. |