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Update read_sequences.rst
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briney committed Oct 18, 2024
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9 changes: 7 additions & 2 deletions docs/source/modules/read_sequences.rst
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Expand Up @@ -8,8 +8,7 @@ read sequences
used file formats. This includes raw sequence data in FASTA or FASTQ format as well as
annotated sequence data in the standard AIRR-C_ format, CSV format, and Parquet format.

.. _AIRR-C: https://docs.airr-community.org/en/stable/datarep/rearrangements.html

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.. table::
:align: left
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for sequence in abutils.io.parse_fastq("sequences.fastq"):
print(sequence)
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``read_fastx()`` and ``parse_fastx()`` are the most flexible and can read/parse either
FASTA or FASTQ files. This is particularly useful when building pipelines in which users
Expand All @@ -83,6 +83,7 @@ may want to process both file types or when the source file may not be known in
for sequence in abutils.io.parse_fastx("sequences.fastq"):
print(sequence)
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All of the FASTA/Q/X ``read`` and ``parse`` functions can handle gzip-compressed files automatically:

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.. autofunction:: abutils.io.read_csv





.. _AIRR-C: https://docs.airr-community.org/en/stable/datarep/rearrangements.html

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